That doesn't make sense..., sorry. Cheers,
Tsjerk On May 21, 2014 6:40 PM, "Chandan Choudhury" <iitd...@gmail.com> wrote: > On Wed, May 21, 2014 at 6:37 PM, Vito Genna <vito.ge...@iit.it> wrote: > > > Dear Tsjerk, > > > > No, it doesn't. (http://wikisend.com/download/324888/Post-nojump.png) > > I think that the first step need to be changed that's why I tried (whit > > no success) > > the flag -pbc whole. I'm still looking for a solution. > > > > > It seems that the tpr you are supplying has PBC in it. I assume the first > tpr should be generated from PBC free structure. That is the understanding > I had. > Correct me if I am wrong. > > Chandan > > > Thanks again. > > > > V > > > > Vito Genna, PhD-Fellow > > Italian Institute of Technology > > Drug Discovery and Development department > > Via Morego 30, 16163 Genoa, Italy > > > > > > > ------------------------------------------------------------------------------------------------------------- > > The process of scientific discovery is, in effect, a continual flight > from > > wonder. > > Albert Einstein > > > > > > ________________________________________ > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [ > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Tsjerk > > Wassenaar [tsje...@gmail.com] > > Sent: Wednesday, May 21, 2014 1:48 PM > > To: Discussion list for GROMACS users > > Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems > > for VMD using > > > > Hey Vito, > > > > After the first step, does the trajectory (say the last frame) look fine? > > If it does (everything nicely assembled), then after the second step, > does > > it still look fine, and is it placed properly in the center of the box? > > > > Cheers, > > > > Tsjerk > > > > > > On Wed, May 21, 2014 at 12:50 PM, Vito Genna <vito.ge...@iit.it> wrote: > > > > > Hi Tsierk, > > > > > > Ok. > > > > > > 1) trjconv_mpi -s em.tpr -f test.xtc -o test-nojump.xtc -pbc nojump > > > (output System) > > > > > > 2) trjconv_mpi -s em.tpr -f test-nojump.xtc -o test-center.xtc -center > -n > > > index.ndx (centering all the frames on different targets Protein/DNA > ecc > > > ecc) (output system) > > > > > > 3) trjconv_mpi -s em.tpr -f test-center.xtc -o test-compact.xtc -pbc > mol > > > -ur rect[or compact] (output System) > > > > > > I also tried, successively, the same procedure adding one step more: - > > pbc > > > whole > > > This last step was added before the step 1. > > > > > > But at the end I obtain the same result. > > > > > > Surely, I'm doing something wrong but I'm not understand what is > > wrong...:/ > > > > > > Thank you for your time. > > > > > > V > > > > > > > > -- > > 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. > > > > > > -- > > -- > Chandan Kumar Choudhury > National Chemical Laboratory, Pune > India > -- > 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.
