Re: [gmx-users] Re: gmx-users Digest, Vol 82, Issue 150
Hi Evelyne, > 1) trjconv -f trajout_dt2000.xtc -s topol.tpr -pbc mol -o trajout_mol.xtc The option -pbc mol IIRC relates to the option for the unit cell representation (-ur). To unbreak molecules using trjconv, you need to have .tpr file and use the option -pbc whole. > 2) trjconv -f trajout_mol.xtc -s topol.tpr -pbc nojump trajout_nojump.xtc > if I use 1) and 2) the system gets "ripped" apart. The system is no longer a > box but a flat disk (very funky) This is because the jumps are removed and over time the lipids diffuse in the plane. They've diffused quite a bit probably, smearing themselves out over a disk. Groetjes, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: gmx-users Digest, Vol 82, Issue 150
ok this does not make sense! Did you check your tpr file? the command 1) should give you a trajectory where the molecules are whole but jumping across the boundaries ... if it does not that means that the tpr is fucky! Try to visualize your tpr in vmd ... night give you some insight on what is going on! You could also make a tpr file ... making sure things a fine :)) On Feb 21, 2011, at 9:45 AM, Evelyne Deplazes wrote: I tried a couple of things according to your suggestions, but no luck so far I used the following commands 1) trjconv -f trajout_dt2000.xtc -s topol.tpr -pbc mol -o trajout_mol.xtc 2) trjconv -f trajout_mol.xtc -s topol.tpr -pbc nojump trajout_nojump.xtc no luck...If I use command 1) only the trajout_mol.xtc the protein is still "split" into to across 2 boxes ie it looks like it did not do anything to the trajectory if I use 1) and 2) the system gets "ripped" apart. The system is no longer a box but a flat disk (very funky) then I tried trjconv -f trajout_dt2000.xtc -s topol.tpr -pbc mol -fit translation -o trajout_fit.xtc again...it looks like the trajectory did not change and the protein is still jumping out of the box then I tried trjconv -f trajout_dt2000.xtc -s topol.tpr -pbc mol -trans -6 6 0 - o trajout_trans.xtc(the box is about 12 x 12) now at least this command did something to the trajectory. The entire protein is now in the center of the box (rather than in the corner) but in the frames where the pb jump occurs the protein still jumps out of the box! it now simply jumps from the center to the next box rather than "sliding" across the border into the next box On 21 February 2011 16:02, wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than "Re: Contents of gmx-users digest..." Today's Topics: 1. Re: g_covar to calculate correlation of motion (Tsjerk Wassenaar) 2. Re: g_covar to calculate correlation of motion (bipin singh) 3. removing pbc jumps from trajectory (Evelyne Deplazes) 4. Re: removing pbc jumps from trajectory (XAvier Periole) -- Forwarded message -- From: Tsjerk Wassenaar To: Discussion list for GROMACS users Date: Mon, 21 Feb 2011 08:14:26 +0100 Subject: Re: [gmx-users] g_covar to calculate correlation of motion Hi Bipin, Try using a .gro or .pdb file as reference structure (-s). Only .tpr files are version specific. Cheers, Tsjerk On Feb 21, 2011 8:05 AM, "bipin singh" wrote: Dear GMX users, I want to calculate the correlated motion between atoms during the md simulation for that purpose I am using g_covar(the one which is available under http://www.gromacs.org/Downloads/User_contributions/Other_software) but it is not compatible with the GROMACS-4.5.3, so please suggest me the alternative way or does anyone have the modified g_covar for GROMKACS-4.5.3. -- - Thanks and regards Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Forwarded message -- From: bipin singh To: Discussion list for GROMACS users Date: Mon, 21 Feb 2011 13:17:48 +0530 Subject: Re: [gmx-users] g_covar to calculate correlation of motion Hi, Thanks for your suggestion. While running the g_covar it is showing the error that aminoacids.dat is not found, so i have copied the residuetypes.dat(which i seems the new modified name for aminoacids.dat in current GROMACS version), then it prompts to choose the group for least square fit, which is not usual groups(i.e protein or C alpha groups etc.).please suggest where i have made mistake. Choose a group for the least squares fit Opening library file aminoacids.dat WARNING 2 [file aminoacids.dat, line 1]: File aminoacids.dat is empty Group 0 ( System) has 30585 elements Group 1 ( GLU) has47 elements Group 2 ( HIS) has86 elements Group 3 ( ASN) has 224 elements Group 4 ( PRO) has56 elements Group 5 ( VAL) has 272 elements Group 6 ( MET) has68 elements Group 7 ( GLY) has 168 elements Group 8 ( ILE) has 190 elements Group 9 ( ALA) has 110 elements Group10 ( SER) has 143 elements Group11 (
[gmx-users] Re: gmx-users Digest, Vol 82, Issue 150
I tried a couple of things according to your suggestions, but no luck so far I used the following commands 1) trjconv -f trajout_dt2000.xtc -s topol.tpr -pbc mol -o trajout_mol.xtc 2) trjconv -f trajout_mol.xtc -s topol.tpr -pbc nojump trajout_nojump.xtc no luck...If I use command 1) only the trajout_mol.xtc the protein is still "split" into to across 2 boxes ie it looks like it did not do anything to the trajectory if I use 1) and 2) the system gets "ripped" apart. The system is no longer a box but a flat disk (very funky) then I tried trjconv -f trajout_dt2000.xtc -s topol.tpr -pbc mol -fit translation -o trajout_fit.xtc again...it looks like the trajectory did not change and the protein is still jumping out of the box then I tried trjconv -f trajout_dt2000.xtc -s topol.tpr -pbc mol -trans -6 6 0 -o trajout_trans.xtc(the box is about 12 x 12) now at least this command did something to the trajectory. The entire protein is now in the center of the box (rather than in the corner) but in the frames where the pb jump occurs the protein still jumps out of the box! it now simply jumps from the center to the next box rather than "sliding" across the border into the next box On 21 February 2011 16:02, wrote: > Send gmx-users mailing list submissions to >gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit >http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to >gmx-users-requ...@gromacs.org > > You can reach the person managing the list at >gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > Today's Topics: > > 1. Re: g_covar to calculate correlation of motion (Tsjerk Wassenaar) > 2. Re: g_covar to calculate correlation of motion (bipin singh) > 3. removing pbc jumps from trajectory (Evelyne Deplazes) > 4. Re: removing pbc jumps from trajectory (XAvier Periole) > > > -- Forwarded message -- > From: Tsjerk Wassenaar > To: Discussion list for GROMACS users > Date: Mon, 21 Feb 2011 08:14:26 +0100 > Subject: Re: [gmx-users] g_covar to calculate correlation of motion > > Hi Bipin, > > Try using a .gro or .pdb file as reference structure (-s). Only .tpr files > are version specific. > > Cheers, > > Tsjerk > > On Feb 21, 2011 8:05 AM, "bipin singh" wrote: > > Dear GMX users, > I want to calculate the correlated motion between atoms during the md > simulation > > for that purpose I am using g_covar(the one which is available under > http://www.gromacs.org/Downloads/User_contributions/Other_software) > > > but it is not compatible with the GROMACS-4.5.3, so please suggest me the > alternative way or does anyone have the modified g_covar for > GROMKACS-4.5.3. > > -- > * > - > Thanks and regards > Bipin Singh > * > * > * > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > > > -- Forwarded message -- > From: bipin singh > To: Discussion list for GROMACS users > Date: Mon, 21 Feb 2011 13:17:48 +0530 > Subject: Re: [gmx-users] g_covar to calculate correlation of motion > Hi, > Thanks for your suggestion. > While running the g_covar it is showing the error that aminoacids.dat is > not found, so i have copied the residuetypes.dat(which i seems the new > modified name for aminoacids.dat in current GROMACS version), then it > prompts to choose the group for least square fit, which is not usual > groups(i.e protein or C alpha groups etc.).please suggest where i have > made mistake. > > Choose a group for the least squares fit > Opening library file aminoacids.dat > WARNING 2 [file aminoacids.dat, line 1]: > File aminoacids.dat is empty > Group 0 ( System) has 30585 elements > Group 1 ( GLU) has47 elements > Group 2 ( HIS) has86 elements > Group 3 ( ASN) has 224 elements > Group 4 ( PRO) has56 elements > Group 5 ( VAL) has 272 elements > Group 6 ( MET) has68 elements > Group 7 ( GLY) has 168 elements > Group 8 ( ILE) has 190 elements > Group 9 ( ALA) has 110 elements > Group10 ( SER) has 143 elements > Group11 ( PHE) has80 elements > Group12 ( LYS) has 242 elements > Group13 ( TYR) has 189 elements > Group14 ( LEU) has 304 elements > Group15 ( GLN) has 102 elements > Group16 ( TRP) has48 elements > Group17 ( ARG) h
