Dear All,
This question is regarding the modified mdrun program i.e mdrun_hole that is
used for creating hole in the lipid bilayer to insert a protein into it.
When I am trying to run the following command:
mdrun_hole -v -hole -holep for_hole.mdp -s run.tpr -o run.trr -x run.xtc
-c after_run.gro -g run.log -e run.edr
though it appears to be running (i.e. even the top command in linux shows
it to be running) but the log file does not show the energy values and
stops at the following point:
####################################################################
There are 6998 molecules, 16413 charge groups and 34175 atoms
There are 0 optimized solvent molecules on node 0
There are 6729 optimized water molecules on node 0
Will do PME sum in reciprocal space.
++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++
U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen
{A smooth particle mesh Ewald method
J. Chem. Phys. 103 (1995) pp. 8577-8592
-------- -------- --- Thank You --- -------- --------
#########################################################################
Also, I have checked the correctness of the tpr file generated by using
simple gromacsv3.1.4 grompp. i.e. when I issue the following command:
mdrun -v -s run.tpr -o run.trr -x run.xtc -c after_run.gro -g run.log -e
run.edr
then it runs properly.
Is there any way of checking whether the mdrun_hole has been installed
properly (although when I write "mdrun_hole -h", it prints out the hole
parameters too, probably telling that mdrun_hole has been installed)?
Has anybody ever faced a similar kind of problem with mdrun_hole?
kindly suggest me something.
waiting for the response,
regards,
Alok.
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