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

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

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>