[gmx-users] Insufficient memory (128 GB) for ensemble entropy calculation with gmx covar/gmx anaeig

[Billy Williams-Noonan]

   Sorry, the original post provides an example of the -dt flag with 100ps
intervals.

On 21 June 2016 at 16:10, Billy Williams-Noonan <
billy.williams-noonan at monash.edu> wrote:

> Thank you for your reply. :)
>
>    My main problem is with gmx covar which does not have a -skip flag.  As
> you can see from the OP I have tried the -dt flag with 250ps intervals.  It
> still crashes due to insufficient memory.  It also crasses with 5000ps
> intervals, giving me just 20ps of frames to work with for the whole
> ensemble.
>
> Billy
>
> On 21 June 2016 at 16:00, David van der Spoel <spoel at xray.bmc.uu.se>
> wrote:
>
>> On 21/06/16 07:34, Billy Williams-Noonan wrote:
>>
>>> Hi Gromacs Users,
>>>
>>>    I am running g_mmpbsa.py to calculate the binding enthalpy of a cyclic
>>> peptide in a drug target.  At the same time I am trying to generate
>>> ensemble estimates for entropy for the protein, ligand and complex.  By
>>> using these two variables I aim to get an idea of the Gibbs free energy
>>> of
>>> binding.
>>>
>>>    My system for the complex and the protein is some 50,000 atoms large,
>>> with just over 3000 atoms belonging to the proteins, and the rest of the
>>> system is water and ions, to make up a physiological concentration of
>>> NaCl.  These are approximate estimates and not exact numbers.  gmx covar
>>> seems to keep crashing every time I try to use it to generate
>>> eigenvectors
>>> for the system.  These are the commands I am using:
>>>
>>>
>>> "  gmx covar -f md.xtc -s md.tpr -v md.eigenvec.trr -av average.pdb
>>> -ascii
>>> covar -xpm covar -xpma covara -l covar -o md.eigenval.xvg -dt 100 -pbc
>>> yes
>>> << EOF
>>> 0
>>> 0
>>> EOF  "
>>>
>>> and:
>>>
>>> "  gmx anaeig -v md.eigenvec.trr -f md.xtc -s md.tpr -entropy -temp 300 >
>>> out.entropy.schlitter  "
>>>
>>>
>>>    I have tried this on a local machine with 16GB of RAM and on a cluster
>>> using one core and a node's worth of RAM (128GB).  I do not have access
>>> to
>>> more RAM than this.  Any ideas on how I can stop my calculation from
>>> crashing due to insufficient memory?
>>>
>> Use the -skip or -dt flags.
>>
>>
>>>    Kind regards,
>>>
>>>    Billy
>>>
>>>
>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
>> --
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>
>
>
> --
> Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon
>
> *LinkedIn Profile
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> **|*   +61420 382 557
>
> Monash Institute for Pharmaceutical Sciences ( *MIPS* )
> Royal Parade, Parkville, 3052
>
>


-- 
Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon

*LinkedIn Profile
<http://www.linkedin.com/profile/preview?locale=en_US&trk=prof-0-sb-preview-primary-button>
**|*   +61420 382 557

Monash Institute for Pharmaceutical Sciences ( *MIPS* )
Royal Parade, Parkville, 3052