Hi Justin, I checked the trjconv help. It also takes .gro files. If so, do I still need to provide a .tpr file? (if yes, then the output can be .gro?)
Payman -----Original Message----- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 22, 2009 6:01 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] genconf Payman Pirzadeh wrote: > 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? No, it does 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! > It can easily be accomplished using a .tpr file, and by using trjconv -pbc whole. After molecules are whole, then use genconf. -Justin > 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 > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== _______________________________________________ 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
