So, "between" or "intra"? "extended intramolecular bonds between cosolvent molecules" Dr. Vitaly V. Chaban
On Wed, Apr 2, 2014 at 8:31 PM, pratibha <kapoorpratib...@gmail.com> wrote: > Hi all > > I have done simulations of my protein in water-cosolvent system (random > initial addition) at 450K. At the end I have used: > trjconv -f *.xtc -s *.tpr -center -pbc whole -o new.xtc > But when I view my trajectory in vmd, I can see extended intramolecular > bonds between cosolvent molecules. This problem usually come when pbc is not > taken care off. But in my case I have used trjconv (as above) to account > this. Is there something wrong in my simulations? I have never encountered > such problem before at lower temperature of 300K. > If needed I can attach my *.mdp file. > > Thanks in advance. > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/extended-bonds-tp5015582.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
