hi, On Friday 01 September 2006 17:16, [EMAIL PROTECTED] wrote: > 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.
have you activated logging? Perhaps set them to nstlog = 1 nstenergy = 1 So every step get logged if this works you can reduce it to normal ones again. Does mdrun generate *.trr file edr ..? > > 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 Greetings, Florian -- ------------------------------------------------------------------------------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26581 Mailto: florian.haberl AT chemie.uni-erlangen.de ------------------------------------------------------------------------------- _______________________________________________ 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