Dear all,
We encountered this error too in our systems, and it probably comes from
"old ages" where some parameters were not dynamically.
Le 09/10/2024 à 17:47, Nikolay Kuzmich via AMBER a écrit :
> I tried to simulate dissociation of protein-protein complex (594aa and 252aa residues) using GaMD (Amber24, ff19SB and OPC3)
> and made the setup according to manual, but immediately after launch the following error occurred:
>
> terminate called after throwing an instance of 'std::runtime_error'
> what(): Too many TI atoms--current limit: 500 atoms
To solve the issue (comments are indicated for previous references of
the discussion, including comments from Bob Duke).
In short, edit the lines in the file src/pmemd/src/gti_controlVariable.i
to for instance double the default values, for instance,
(1) increase STATIC_CONST_INT MaxNumberTIAtom rom 500 to 1000
STATIC_CONST_INT MaxNumberTIAtom = 1000;
(2) increase STATIC_CONST_INT MaxNumberTIPair from 300 to 600
STATIC_CONST_INT MaxNumberTIPair = 600;
(3) increase STATIC_CONST_INT MaxNumberREAFAtom from 500 to 1000
STATIC_CONST_INT MaxNumberREAFAtom = 1000;
(4) compile the modifed code, install it, and the problem should disappear.
HTH,
Stéphane
.amber developpers, here is a patch below (with comments in refering
threads) that may be applied for future patch / releases of AMBER?
#
https://sourceforge.net/p/gamd/mailman/gamd-discuss/thread/BN0PR01MB68323106A2B4CA8D228F60C8AAB99%40BN0PR01MB6832.prod.exchangelabs.com/#msg37673406
#
https://github.com/GHeinzelmann/BAT.py/issues/12
#
https://sourceforge.net/p/gamd/mailman/gamd-discuss/thread/VI1PR07MB615977345DB5F49E7DEC367AEEB99%40VI1PR07MB6159.eurprd07.prod.outlook.com/#msg37673311
me.mymachine:~/tmp/amber22_src$ diff -Naup
./src/pmemd/src/gti_controlVariable.i-orig
./src/pmemd/src/gti_controlVariable.i
--- ./src/pmemd/src/gti_controlVariable.i-orig 2023-10-04
18:05:07.200713487 +0200
+++ ./src/pmemd/src/gti_controlVariable.i 2023-10-04
18:05:27.624773622 +0200
.. -7,11 +7,11 ..
#define STATIC_CONST_INT integer, parameter::
#endif
- STATIC_CONST_INT MaxNumberTIAtom = 500;
- STATIC_CONST_INT MaxNumberTIPair = 300;
+ STATIC_CONST_INT MaxNumberTIAtom = 1000;
+ STATIC_CONST_INT MaxNumberTIPair = 600;
STATIC_CONST_INT MaxNumberNBPerAtom = 3072;
- STATIC_CONST_INT MaxNumberREAFAtom = 500;
+ STATIC_CONST_INT MaxNumberREAFAtom = 1000;
STATIC_CONST_INT GPUPotEnergyTerms = 54;
STATIC_CONST_INT NumberTIEnergyTerms = 17;
--
Associate Professor, USBB, UMR 6286 CNRS, Bioinformatique Structurale
UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France
Tél : +33 251 125 636 / Fax : +33 251 125 632
http://www.us2b.univ-nantes.fr/ -http://www.steletch.org
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Received on Mon Dec 09 2024 - 01:30:03 PST
