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

[David van der Spoel]

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