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

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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...<mailto: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::MaxNumberTIAtom2 + 1) *
cuda/gti_NBList_kernels.cu://                                    gti_simulationConst::MaxNumberTIAtom2];
cuda/gti_NBList_kernels.cu://  __shared__ volatile float coordTI[gti_simulationConst::MaxNumberTIAtom2][3];
cuda/gti_NBList_kernels.cu:    __shared__ volatile bool bondMask[(MaxNumberTIAtom2 + 1) *
cuda/gti_NBList_kernels.cu:                                              MaxNumberTIAtom2];
cuda/gti_NBList_kernels.cu:    __shared__ volatile float coordTI[MaxNumberTIAtom2][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...<mailto: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...<mailto: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<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...<mailto:cgs...@gm...>> wrote:

You don't often get email from cgs...@gm...<mailto: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...<mailto:cg...@uc...>
[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...<mailto:cg...@uc...>
[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...<mailto:cg...@uc...>
[www.linkedin.com/in/christianseitz21]<http://www.linkedin.com/in/christianseitz21>