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. _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php