Hi Stephane,
thank you, I will try it.
Merci beaucoup,
Nick
Stéphane Téletchéa via AMBER <amber.ambermd.org> schrieb am Mo., 9. Dez.
2024, 11:11 AM:
> 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 - 12:00:02 PST
