Re: [GaMD-discuss] error with amber24 GaMD-PPI Too many TI atoms--current limit: 500 atoms

[Christian S. <cgs...@gm...>]

Hi Yinglong,

Good to know that anything in ambmask format should work. Victor, do you
have recommendations on how to segment a GaMD equilibration run into
multiple parts?

best,
Christian

On Mon, Nov 24, 2025 at 6:48 PM Miao, Yinglong <Yin...@me...>
wrote:

> Hi Christian,
>
> Great that your system runs with PPI-GaMD by “only modifying the
> MaxNumberTIAtom”. Thanks for confirming that!
>
> Note that timask1 and scmask1 use atom masks. Anything in the *ambmask
> format* should work; it doesn’t have to be defined by residues.
> You can find detailed descriptions of PPI-GaMD simulation parameters in
> the paper SI: https://pubs.acs.org/doi/10.1021/acs.jctc.1c00974.
>
> Victor can probably comment more on your questions as well.
>
> Best,
> Yinglong
>
>
> On Nov 24, 2025, at 7:06 PM, Christian Seitz <cgs...@gm...> wrote:
>
> Hi Victor and Yinglong,
>
> Victor, thanks for this information. I have a few more questions. For
> clarity, let's say that protein 1 is a small antibody, protein 2 is a large
> glycoprotein, and I want to see association/dissociation between the two.
>
> 1) You are saying that I should select the interfacial residues of protein
> 1, and then all the atoms of protein 2? I was under the impression that I
> should select all residues of protein 1, because the GaMD-AMBER manual
> defines "timask1" as "Specifies atoms of the first (bound) ligand or
> peptide in ambmask format...". A similar definition is given for "scmask1".
> But this should be just the interfacial residues, not the entire antibody?
> And they should be given as residues, not atoms? If so, perhaps the manual
> could be revised for clarity.
> 2) I ran x ns of a GaMD equilibration, and am ready to run another part.
> Thus I should subtract x ns from the overall GaMD equilibration run, as
> that is already complete. Do I subtract x ns from the normal MD
> equilibration (ntcmdprep)? Or the biasing MD equilibration (ntebprep), or
> perhaps something else? Overall, does the equilibration go from
> ntcmdprep -> ntebprep -> ntcmd -> nteb, or what order of steps does the
> equilibration run through? This will let me know how to modify my
> equilibration input files for restarted equilibration runs.
>
> Yinglong, good catch from Jinan. I recompiled amber24, only modifying the
> MaxNumberTIAtom = 750 -> 5250, and my system runs with this. Contrary to
> answers I've seen elsewhere, I can leave MaxNumberTIPair and
> MaxNumberREAFAtom at their default values and my system will run GaMD-PPI.
> In my GaMD equilibration run, at least, my system does not run any faster
> by leaving MaxNumberTIPair and MaxNumberREAFAtom at their default values.
>
> Thanks for your help!
>
> Best,
> Christian
>
> On Sun, Nov 23, 2025 at 9:11 AM Miao, Yinglong <Yin...@me...>
> wrote:
>
>> Hi Christian,
>>
>> I’m glad that your new simulation works. Jinan mentioned that the
>> “essential" code change in Amber for running PPI-GaMD would be increase in “
>> MaxNumberTIAtom", in your case:
>>
>> MaxNumberTIAtom = 750 -> 5250
>>
>>
>> Could you do us a favor to double check if that’s “sufficient", and other
>> changes are not necessary?
>>
>> Thanks,
>> Yinglong
>>
>>
>> On Nov 18, 2025, at 9:25 AM, Adediwura, Victor Ayo <
>> vad...@em...> wrote:
>>
>> Hi Christian,
>>
>> Glad to hear that the code works!
>>
>> A few comments, the timask1 and scmask1 should be residue number rather
>> than atom numbers. timask1 and scmask1 are the region you would like to see
>> boosted (e.g for protein-protein dissociation, this could be the
>> interfacial residues of the first protein).  The bgpro2atm and edpro2atm
>> should be the first atom number of the second protein, and edpro2atm is the
>> last atom of the second protein (which is also boosted). Thus, for the
>> first protein, you will have to select interface residues for boosting
>> while for the second protein, you would have to select from the first to
>> the last atom for boosting. In essence, you might want to renumber your PDB
>> such that the first protein where you are selecting some part of the
>> protein (i.e interfacial residues) should come last and the second protein
>> would come first
>>
>>
>> For the second part, I would suggest to run longer equilibration
>> considering size of your system which is quite large. For how it will play
>> out in this case, I think this is a good idea " If I were to break up one
>> long GaMD equilibration, how would I do so? Just change restart parameters,
>> i.e. irest=1, ntx=5, as if I were restarting a normal, production MD?"
>>
>> I hope this helps!
>>
>> Kind regards,
>>
>> Victor
>>
>>
>>
>> ------------------------------
>> *From:* Christian Seitz <cgs...@gm...>
>> *Sent:* Monday, November 17, 2025 6:18 PM
>> *To:* Adediwura, Victor Ayo <vad...@em...>
>> *Cc:* Miao, Yinglong <Yin...@me...>; gamd-discuss <
>> gam...@li...>; Davis, James J. <jj...@an...>;
>> Ramanathan, Arvind <ram...@an...>
>> *Subject:* Re: [GaMD-discuss] error with amber24 GaMD-PPI Too many TI
>> atoms--current limit: 500 atoms
>>
>> Hi Victor,
>>
>> Fantastic, this works! The key change was involving all atoms in the TI
>> mask, not excluding hydrogens:
>>
>> timask1 = ':1870-2126!@H' -> timask1 = ':1870-2126'
>> scmask1 = ':1870-2126!@H' -> scmask1 = ':1870-2126'
>>
>> I would have thought that including the hydrogens in the TI mask would
>> increase the atom limit of the system, and thus push it closer to amber24's
>> TI atom limit. For my own understanding, do you know why including
>> hydrogens in the TI mask allowed the system to run?
>>
>> Separately, I do not think I can finish a full GaMD equilibration for
>> each of my systems within my computing resource's wallclock limit. Would it
>> be better to run multiple short GaMD equilibrations until the k0P and k0D
>> stabilize at 1.0, or should I run one longer GaMD equilibration and break
>> it up into multiple runs? If I were to break up one long GaMD
>> equilibration, how would I do so? Just change restart parameters, i.e.
>> irest=1, ntx=5, as if I were restarting a normal, production MD?
>>
>> Many thanks for your help in this.
>>
>> Best,
>> Christian
>>
>> On Sat, Nov 15, 2025 at 12:00 PM Adediwura, Victor Ayo <
>> vad...@em...> wrote:
>>
>> Hi Christian,
>>
>> I just checked the files and noticed there is an issue with the
>> equil_gamd.in file. I have modified this file, and it should work. Pls
>> find attached the modify file.
>>
>> Kind regards,
>>
>> Victor
>>
>>
>> ------------------------------
>> *From:* Miao, Yinglong via GaMD-discuss <
>> gam...@li...>
>> *Sent:* Monday, November 10, 2025 8:48 PM
>> *To:* Christian Seitz <cgs...@gm...>
>> *Cc:* gamd-discuss <gam...@li...>; Davis, James J.
>> <jj...@an...>; Ramanathan, Arvind <ram...@an...>
>> *Subject:* Re: [GaMD-discuss] error with amber24 GaMD-PPI Too many TI
>> atoms--current limit: 500 atoms
>>
>> Hi Christian,
>>
>> It might be better to select all atoms in the protein 1 for timask1 and
>> scmask1.
>>
>> Other than that, what you changed especially under 2) should have
>> resolved the issue. Could you possibly share your simulation input files
>> and the mdout file? We’d like to run it with our local Amber and see how it
>> works.
>>
>> Best,
>> Yinglong
>>
>>
>> On Nov 10, 2025, at 4:07 PM, Christian Seitz <cgs...@gm...> wrote:
>>
>> Hi Yinglong,
>>
>> Thanks for the suggestions. I have tried several things so far, let me
>> recap them. My system contains 1,951 heavy atoms (3,814 atoms total) in the
>> TI region, which I am calling through timask1 = ':1870-2126!@H' and scmask1
>> = ':1870-2126!@H' in an input file to run GaMD-PPI.
>>
>> 1) I compiled a standard, unmodified build of amber24. When I put a large
>> system into that build to run GaMD-PPI, I get an error saying that the TI
>> atom limit is 500 atoms. Thus I need to expand the TI atom limit.
>>
>> 2) I tried changing the "MaxNumberTIAtom", "MaxNumberTIPair", and
>> "MaxNumberREAFAtom"
>> within $AMBERHOME/amber/pmemd24_src/src/pmemd/src/gti_controlVariable.i. I
>> increased these atom limits as shown below, recompiled a fresh version of
>> amber24, and still found the same error, saying the atom limit in TI was
>> 500.
>>
>> MaxNumberTIAtom = 750 -> 5250
>> MaxNumberTIPair = 300 -> 3000
>> MaxNumberREAFAtom = 500 -> 4000
>>
>> 3) The "MaxNumberTIAtom2"
>> within $AMBERHOME/amber/pmemd24_src/src/pmemd/src//cuda/gti_NBList_kernels.cu
>> comes with a limit of 4000, which should be enough for this system.
>>
>> static const int MaxNumberTIAtom2 = 4000
>>
>> I did not try increasing that.
>>
>> Do you have any idea what might be overwriting these other variables to
>> enforce a smaller TI atom limit? I'm thinking the error message, stating
>> there's a TI atom limit of 500, is probably not tied to the actual TI atom
>> limit - I'm guessing that if one made the TI atom limit to be 2 atoms, the
>> error message would still say the TI atom limit is 500. But I cannot figure
>> out what variable is actually controlling the TI atom limit, or how to
>> increase that. Or perhaps there's some issue with how I'm telling GaMD-PPI
>> to select my TI atoms, and it's selecting more than I want? I can send my
>> input files or system files if that helps, or can try any other ideas you
>> have to get this to run. Thanks for your help!
>>
>> Best,
>> Christian
>>
>> On Mon, Nov 10, 2025 at 6:11 AM Miao, Yinglong <Yin...@me...>
>> wrote:
>>
>> Hi Christian,
>>
>> The related parameters should be defined in file
>> *$AMBERHOME/src/pmemd/src/gti_controlVariable.i*. I compared this file
>> in our "gamd" branch with master branch in the Amber git repository:
>>
>> *# AMBER “gamd"*
>>
>> *  STATIC_CONST_INT MaxNumberTIAtom **=* *4000**;*
>> *  STATIC_CONST_INT MaxNumberTIPair **=* *3000**;*
>>   STATIC_CONST_INT MaxNumberNBPerAtom = 3072;
>>
>> *  STATIC_CONST_INT MaxNumberREAFAtom **=* *5000**;*
>>   STATIC_CONST_INT MaxNumberRMSDAtom = 200;
>>   STATIC_CONST_INT MaxNumberRMSDRegion = 5;
>>
>>
>> *# AMBER master*
>>
>>   STATIC_CONST_INT MaxNumberTIAtom = 750;
>>   STATIC_CONST_INT MaxNumberTIPair = 300;
>>   STATIC_CONST_INT MaxNumberNBPerAtom = 3072;
>>
>>   STATIC_CONST_INT MaxNumberREAFAtom = 500;
>>   STATIC_CONST_INT MaxNumberRMSDAtom = 200;
>>   STATIC_CONST_INT MaxNumberRMSDRegion = 5;
>>
>> Three parameters “*MaxNumberTIAtom*”, “*MaxNumberTIPair*” and “
>> *MaxNumberREAFAtom*” are modified. Could you help to try those values as
>> used in the “gamd” branch to see if that resolves the issue?
>>
>> Thanks,
>> Yinglong
>>
>>
>>
>> On Nov 9, 2025, at 11:44 AM, Miao, Yinglong <Yin...@me...>
>> wrote:
>>
>> Hi Christian,
>>
>> Seems you are changing these variables in the wrong direction. You need to
>>  *increase* *MaxNumberTIAtom *and *MaxNumberTIAtom2 *to a number greater
>> than 500, like 4000 or the number of atoms in your protein 1 for simulation.
>>
>> Hope this helps,
>> Yinglong
>>
>>
>>
>> On Nov 5, 2025, at 5:16 PM, Christian Seitz <cgs...@gm...> wrote:
>>
>> Hi Yinglong,
>>
>> Thanks, as a test I reduced the limit in
>> $AMBERHOME/amber/pmemd24_src/src/pmemd/src//cuda/gti_NBList_kernels.cu from
>> 4000 to 400:
>>
>> static const int MaxNumberTIAtom2 = 4000 -> 400
>>
>> After building a fresh install of amber24 with this reduced atom limit, I
>> found that the TI atom limit remained at 500. If it helps, inside
>> $AMBERHOME/amber/pmemd24_src/src/pmemd/src/cuda/gti_gpuContext.cpp one can
>> find this snippet:
>>
>>  if (TISize > gti_simulationConst::MaxNumberTIAtom) {
>>           std::string e("Too many TI atoms--current limit: 500 atoms");
>>           throw std::runtime_error(e);
>>
>> I can only find TISize
>> in $AMBERHOME/amber/pmemd24_src/src/pmemd/src/cuda/gti_gpuContext.cpp. I
>> have tried grepping a variety of terms
>> within $AMBERHOME/amber/pmemd24_src/src/pmemd/src, such as "500",
>> "TIAtoms", and "TISize", but nothing amongst these stand out to my
>> non-expert eyes to change. When I ask chatgpt or claude how to solve this,
>> they simply refer to the forum posts in my initial email, including this
>> post, and suggest searching through non-existent files. Do you have any
>> other ideas on where to search or what to look for? Thanks for your help!
>>
>> Best,
>> Christian
>>
>>
>> On Mon, Nov 3, 2025 at 7:57 PM Miao, Yinglong <Yin...@me...>
>> wrote:
>>
>> Hi Christian,
>>
>> This is what I found for “MaxNumberTIAtom” in the pmemd src code:
>>
>> *~/amber-git/src/pmemd/src*$ grep -iR "MaxNumberTIAtom" *
>> cuda/gti_NBList_kernels.cu:  __shared__ volatile float
>> coordTI[gti_simulationConst::*MaxNumberTIAtom*][3];
>> cuda/gti_NBList_kernels.cu:  __shared__ float
>> coordTI[gti_simulationConst::*MaxNumberTIAtom*][3];
>> cuda/gti_NBList_kernels.cu:  __shared__ volatile float
>> coordTI[gti_simulationConst::*MaxNumberTIAtom*][3];
>> *cuda/gti_NBList_kernels.cu:  static const int MaxNumberTIAtom2 = 4000;*
>> cuda/gti_NBList_kernels.cu://  __shared__ volatile bool
>> bondMask[(gti_simulationConst::*MaxNumberTIAtom*2 + 1) *
>> cuda/gti_NBList_kernels.cu://
>> gti_simulationConst::*MaxNumberTIAtom*2];
>> cuda/gti_NBList_kernels.cu://  __shared__ volatile float
>> coordTI[gti_simulationConst::*MaxNumberTIAtom*2][3];
>> cuda/gti_NBList_kernels.cu:    __shared__ volatile bool bondMask[(
>> *MaxNumberTIAtom*2 + 1) *
>> cuda/gti_NBList_kernels.cu:
>> *MaxNumberTIAtom*2];
>> cuda/gti_NBList_kernels.cu:    __shared__ volatile float coordTI[
>> *MaxNumberTIAtom*2][3];
>> cuda/gti_gpuContext.cpp:  uint4 *temp = new uint4[gti_simulationConst::
>> *MaxNumberTIAtom*];
>> cuda/gti_gpuContext.cpp:  unsigned* tempSC = new
>> unsigned[gti_simulationConst::*MaxNumberTIAtom**2];
>> cuda/gti_gpuContext.cpp:  unsigned tempShift = gti_simulationConst::
>> *MaxNumberTIAtom*;
>> cuda/gti_gpuContext.cpp:        if (TISize > gti_simulationConst::
>> *MaxNumberTIAtom*) {
>> cuda/gti_gpuContext.cpp:  int tempList[gti_simulationConst::
>> *MaxNumberTIAtom*];
>> *gti_controlVariable.i:  STATIC_CONST_INT MaxNumberTIAtom = 4000;*
>> ti.F90:  !!integer, parameter::*MaxNumberTIAtom*=500 !! this must be
>> consistent w/ gti_controlVariable.i
>>
>> Maybe you can check *MaxNumberTIAtom2 in **cuda/gti_NBList_kernels.cu *as
>> well?
>>
>> Best,
>> Yinglong
>>
>>
>> On Oct 31, 2025, at 6:28 PM, Christian Seitz <cgs...@gm...> wrote:
>>
>> Hi Yinglong,
>>
>> Thanks for the helpful example, I tried a couple more things:
>> 1) I tried compiling amber24 in several different places, all while
>> editing the
>> $AMBERHOME/amber/pmemd24_src/src/pmemd/src/gti_controlVariable.i file to
>> match what you sent. Each time I tried a run, I found the error saying the
>> TI atom limit is 500.
>> 2) I tried compiling amber24 without editing any files. This means the
>> default MaxNumberTIAtom is 750 inside
>> $AMBERHOME/amber/pmemd24_src/src/pmemd/src/gti_controlVariable.i. When I
>> try to run GaMD-PPI with this version, my system still crashes with a TI
>> atom limit of 500.
>>
>> Am I missing something? In amber24 is there another variable that
>> overrides the limits set inside the gti_controlVariable.i file? If so, that
>> would explain why running GaMP-PPI shows an atom limit of 500 even though
>> the default amber24 TI atom limit inside gti_controlVariable.i is 750. In
>> 2) the only file I edited was the
>> $AMBERHOME/amber/pmemd24_src/build/run_cmake file, where I edited the linux
>> section to be
>>
>>   cmake $AMBER_PREFIX/pmemd24_src \
>>     -DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/pmemd24 \
>>     -DCOMPILER=MANUAL  \
>>     -DMPI=TRUE -DCUDA=TRUE -DINSTALL_TESTS=TRUE \
>>     -DDOWNLOAD_MINICONDA=FALSE -DBUILD_PYTHON=FALSE \
>>     -DBUILD_PERL=FALSE -DBUILD_GUI=FALSE \
>>     -DPMEMD_ONLY=TRUE -DCHECK_UPDATES=FALSE \
>>     -DDISABLE_TOOLS=FEW -DCMAKE_C_COMPILER=gcc-12 \
>>     -DCMAKE_CXX_COMPILER=g++-12 -DCMAKE_Fortran_COMPILER=gfortran-12 \
>>     2>&1 | tee  cmake.log
>>
>> to compile on the resource I am using. Let me know if there are any files
>> I can send to help diagnose this~
>>
>> Best,
>> Christian
>>
>> On Thu, Oct 30, 2025 at 10:56 AM Miao, Yinglong <
>> Yin...@me...> wrote:
>>
>> Hi Christian,
>>
>> Sorry for the issue with running PPI-GaMD. To perhaps follow up with the
>> post by Dr. Fabian Glaser as you mentioned in your email, I’m attaching
>> more detailed discussion he had later on with Jinan to resolve the issue.
>>
>> Hope the example “gti_controlVariable.i” and the idea of using “only the
>> interfacial atoms of the first protein in TIMASK1/SCMASK1, and then the
>> second FULL protein first and last atoms in bgpro2atm and edprod2atm” could
>> help.
>>
>> For “bgpro2atm and edpro2atm”, it would make sense to include ALL atoms
>> associated with the second protein, including the PTMs.
>>
>> Best,
>> Yinglong
>>
>>
>>
>> Yinglong Miao, Ph.D.
>> Associate Professor
>> Department of Pharmacology and
>> Computational Medicine Program
>> University of North Carolina - Chapel Hill
>> Tel: 1-919-962-5696
>> http://miaolab.org
>>
>> Editor-in-Chief
>> *npj Drug Discovery*
>> https://www.nature.com/npjdrugdiscov
>>
>> On Oct 29, 2025, at 5:03 PM, Christian Seitz <cgs...@gm...> wrote:
>>
>> You don't often get email from cgs...@gm.... Learn why this is
>> important <https://aka.ms/LearnAboutSenderIdentification>
>> Hello Yinglong + co,
>>
>> I am trying to equilibrate a system for use in GaMD-PPI using amber24. I
>> ran it through normal equilibration for MD (heating, minimizing,
>> equilibration) already. I tried to start a GaMD equilibration, but
>> immediately the system fails with a segfault:
>>
>> terminate called after throwing an instance of 'std::runtime_error'
>>   what():  Too many TI atoms--current limit: 500 atoms
>>
>> I went
>> into $AMBERHOME/amber/pmemd24_src/src/pmemd/src/gti_controlVariable.i and
>> changed the following parameters:
>>
>> MaxNumberTIAtom = 750 -> 5250
>> MaxNumberTIPair = 300 -> 3000
>> MaxNumberREAFAtom = 500 -> 4000
>>
>> I can make a fresh build of amber24 and compile with these adjusted
>> parameters, but running it still results in a TI atom limit of 500 atoms.
>> This issue was seen previously here
>> <http://archive.ambermd.org/202412/0029.html>, here
>> <https://sourceforge.net/p/gamd/mailman/gamd-discuss/thread/SA1PR03MB6450A4FB3834171AE436C154B85F2%40SA1PR03MB6450.namprd03.prod.outlook.com/#msg58743189>
>> , here <http://archive.ambermd.org/202206/0050.html>, and here
>> <http://archive.ambermd.org/202307/0086.html>. It appears one person
>> <https://sourceforge.net/p/gamd/mailman/gamd-discuss/thread/36223A2E-0AC1-4D6B-8F42-E1B5C996FE4F%40uconn.edu/>
>>  was able to fix this issue in a previous version of amber, but not
>> amber24. Do you have any ideas on what other parameters I would need to
>> modify to increase the TI atom limit? Thank you!
>>
>> I also have a question about the atom masks. When I select the atom mask
>> bgpro2atm and edpro2atm, should this mask only include protein atoms or
>> also PTMs, such as glycans, attached to the protein?
>>
>> Thanks for your help!
>>
>> Best,
>> Christian
>>
>> --
>> *Christian Seitz*
>> PhD, Biochemistry & Biophysics | UCSD
>> Postdoc, Computer Science | UChicago
>> cgs...@gm... <cg...@uc...>
>> [image: www.linkedin.com/in/christianseitz21]
>> <http://www.linkedin.com/in/christianseitz21>
>> _______________________________________________
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>>
>>
>>
>>
>> --
>> *Christian Seitz*
>> PhD, Biochemistry & Biophysics | UCSD
>> Postdoc, Computer Science | UChicago
>> cgs...@gm... <cg...@uc...>
>> [image: www.linkedin.com/in/christianseitz21]
>> <http://www.linkedin.com/in/christianseitz21>
>> _______________________________________________
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>>
>>
>>
>>
>> --
>> *Christian Seitz*
>> PhD, Biochemistry & Biophysics | UCSD
>> Postdoc, Computer Science | UChicago
>> cgs...@gm... <cg...@uc...>
>> [image: www.linkedin.com/in/christianseitz21]
>> <http://www.linkedin.com/in/christianseitz21>
>>
>>
>>
>>
>>
>> --
>> *Christian Seitz*
>> PhD, Biochemistry & Biophysics | UCSD
>> Postdoc, Computer Science | UChicago
>> cgs...@gm... <cg...@uc...>
>> [image: www.linkedin.com/in/christianseitz21]
>> <http://www.linkedin.com/in/christianseitz21>
>>
>>
>>
>>
>> --
>> *Christian Seitz*
>> PhD, Biochemistry & Biophysics | UCSD
>> Postdoc, Computer Science | UChicago
>> cgs...@gm... <cg...@uc...>
>>
>>
>>
>
> --
> *Christian Seitz*
> PhD, Biochemistry & Biophysics | UCSD
> Postdoc, Computer Science | UChicago
> cgs...@gm... <cg...@uc...>
> [image: www.linkedin.com/in/christianseitz21]
> <http://www.linkedin.com/in/christianseitz21>
> _______________________________________________
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-- 
*Christian Seitz*
PhD, Biochemistry & Biophysics | UCSD
Postdoc, Computer Science | UChicago
cgs...@gm... <cg...@uc...>
[image: www.linkedin.com/in/christianseitz21]
<http://www.linkedin.com/in/christianseitz21>