Hello, I minimized the initial output (from another simulation) first; then I replicated it. This time, the minimization of the bigger box was done more easily! I ran an MD simulation with the bigger box and after 6 hours, it has not crashed yet. But, I have a question. When we replicate a box, and in the primary box one molecule is dissected into pieces due to pbc, will GROMACS return the molecules to its original shape during MD run or not? I believe, without minimization, these dissected pieces will remain in the middle of the box and interfere with their replicated versions. Maybe, 'genconf' should be modified for such replications to maintain the pbc between the new molecules at the boundaries and fix the problem with the particle in the middle of the new bigger box!
Payman -----Original Message----- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Payman Pirzadeh Sent: July 22, 2009 9:22 AM To: 'Discussion list for GROMACS users' Subject: RE: [gmx-users] genconf Thanks a lot Mark! I will run the system for equilibration and then try to replicate it. I will keep you guys posted. Payman -----Original Message----- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: July 21, 2009 11:01 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] genconf Payman Pirzadeh wrote: > Yes and no! > Sometimes there is an overlap, but sometimes I could find nothing! In the > simplest case, how can we avoid overlaps in a way that the crystal structure > is maintained under pbc? > Can the option "-dist" help here? Replicating a box that was not designed for periodicity will always have this problem. Whether the box is too small or two large, there will either be steric clashes, or vacuums that will need filling. The general solution is to equilibrate your box under PBC prior to replication. Now the box size and the atomic spacings will be plausible, and the replication will not of necessity introduce artifacts. Mark _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
