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

[Billy Williams-Noonan]

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?

   Kind regards,

   Billy

-- 
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