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

[Billy Williams-Noonan]

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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