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

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

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>