Re: [gmx-users] Re: how to show dodecahedron box in VMD
Thanks lot. Happy Thanksgiving!. -Xianghong Qi On Wed, Nov 26, 2008 at 8:53 AM, Alessandro Casoni < [EMAIL PROTECTED]> wrote: > Tsjerk Wassenaar ha scritto: > >> Hi, >> >> Can't help you with VMD, but I do have a script to take care of this in >> Pymol. >> >> Cheers, >> >> Tsjerk >> >> On 11/25/08, xianghong qi <[EMAIL PROTECTED]> wrote: >> >> >>> Dear all: >>> >>> I am trying to show the dodecahedron box only in vmd since my simulation >>> box >>> is dodecahedron. If I include water, I can see the box is dodecahedron. >>> But >>> I want to get rid off all of water, then my box will not appear there. >>> How >>> can I keep the dodecahedron box boundaries and solute only? Looks like >>> only >>> the rectangular box boundaries can be drawn in VMD. >>> Does anyone has some suggestions? Appreciate your great help. >>> Happy Thanksgiving. >>> -Xianghong Qi >>> >>> -- >>> Some people make the world more special just by being in it. >>> >>> ___ >>> gmx-users mailing listgmx-users@gromacs.org >>> http://www.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 [EMAIL PROTECTED] >>> Can't post? Read >>> http://www.gromacs.org/mailing_lists/users.php >>> >>> >>> >> >> >> >> > Hi, > you can try this: > > trjconv -f ?.trr -s ?.tpr -o output.trr *-pbc mol -ur compact* > > or > > trjconv -f ?.trr -s ?.tpr -o output.gro *-pbc mol -ur compact* -e 1 > > well...the first converts all your trajectory and the last command extracts > 1 frame in a gro file.. > > good luck > alessandro > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Some people make the world more special just by being in it. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: how to show dodecahedron box in VMD
Tsjerk Wassenaar ha scritto: Hi, Can't help you with VMD, but I do have a script to take care of this in Pymol. Cheers, Tsjerk On 11/25/08, xianghong qi <[EMAIL PROTECTED]> wrote: Dear all: I am trying to show the dodecahedron box only in vmd since my simulation box is dodecahedron. If I include water, I can see the box is dodecahedron. But I want to get rid off all of water, then my box will not appear there. How can I keep the dodecahedron box boundaries and solute only? Looks like only the rectangular box boundaries can be drawn in VMD. Does anyone has some suggestions? Appreciate your great help. Happy Thanksgiving. -Xianghong Qi -- Some people make the world more special just by being in it. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Hi, you can try this: trjconv -f ?.trr -s ?.tpr -o output.trr *-pbc mol -ur compact* or trjconv -f ?.trr -s ?.tpr -o output.gro *-pbc mol -ur compact* -e 1 well...the first converts all your trajectory and the last command extracts 1 frame in a gro file.. good luck alessandro ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: how to show dodecahedron box in VMD
Hi, Can't help you with VMD, but I do have a script to take care of this in Pymol. Cheers, Tsjerk On 11/25/08, xianghong qi <[EMAIL PROTECTED]> wrote: > Dear all: > > I am trying to show the dodecahedron box only in vmd since my simulation box > is dodecahedron. If I include water, I can see the box is dodecahedron. But > I want to get rid off all of water, then my box will not appear there. How > can I keep the dodecahedron box boundaries and solute only? Looks like only > the rectangular box boundaries can be drawn in VMD. > Does anyone has some suggestions? Appreciate your great help. > Happy Thanksgiving. > -Xianghong Qi > > -- > Some people make the world more special just by being in it. > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.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 [EMAIL PROTECTED] > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: how to show dodecahedron box in VMD
Dear all: I am trying to show the dodecahedron box only in vmd since my simulation box is dodecahedron. If I include water, I can see the box is dodecahedron. But I want to get rid off all of water, then my box will not appear there. How can I keep the dodecahedron box boundaries and solute only? Looks like only the rectangular box boundaries can be drawn in VMD. Does anyone has some suggestions? Appreciate your great help. Happy Thanksgiving. -Xianghong Qi -- Some people make the world more special just by being in it. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
