<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br></div><div>ok this does not make sense! Did you check your tpr file?</div><div>the command 1) should give you a trajectory where the molecules</div><div>are whole but jumping across the boundaries ... if it does not that </div><div>means that the tpr is fucky! </div><div><br></div><div>Try to visualize your tpr in vmd ... night give you some insight on what is </div><div>going on! </div><div><br></div><div>You could also make a tpr file ... making sure things a fine :)) </div><div><br></div><div><div>On Feb 21, 2011, at 9:45 AM, Evelyne Deplazes wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">I tried a couple of things according to your suggestions, but no luck so far <br><br>I used the following commands <br>1) trjconv -f trajout_dt2000.xtc -s topol.tpr -pbc mol -o trajout_mol.xtc <br> 2) trjconv -f trajout_mol.xtc -s topol.tpr -pbc nojump trajout_nojump.xtc <br><br>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<br> if I use 1) and 2) the system gets "ripped" apart. The system is no longer a box but a flat disk (very funky)<br><br><br>then I tried <br>trjconv -f trajout_dt2000.xtc -s topol.tpr -pbc mol -fit translation -o trajout_fit.xtc<br> again...it looks like the trajectory did not change and the protein is still jumping out of the box <br><br>then I tried <br>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) <br> 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<br><br><div class="gmail_quote">On 21 February 2011 16:02, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br> <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Send gmx-users mailing list submissions to<br> <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br> <br> To subscribe or unsubscribe via the World Wide Web, visit<br> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br> or, via email, send a message with subject or body 'help' to<br> <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br> <br> You can reach the person managing the list at<br> <a href="mailto:gmx-users-owner@gromacs.org">gmx-users-owner@gromacs.org</a><br> <br> When replying, please edit your Subject line so it is more specific<br> than "Re: Contents of gmx-users digest..."<br> <br>Today's Topics:<br> <br> 1. Re: g_covar to calculate correlation of motion (Tsjerk Wassenaar)<br> 2. Re: g_covar to calculate correlation of motion (bipin singh)<br> 3. removing pbc jumps from trajectory (Evelyne Deplazes)<br> 4. Re: removing pbc jumps from trajectory (XAvier Periole)<br> <br><br>---------- Forwarded message ----------<br>From: Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>><br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br> Date: Mon, 21 Feb 2011 08:14:26 +0100<br>Subject: Re: [gmx-users] g_covar to calculate correlation of motion<br><p>Hi Bipin,</p><p>Try using a .gro or .pdb file as reference structure (-s). Only .tpr files are version specific.</p><p>Cheers,</p><p>Tsjerk</p><div><br class="webkit-block-placeholder"></div><blockquote type="cite">On Feb 21, 2011 8:05 AM, "bipin singh" <<a href="mailto:bipinelmat@gmail.com" target="_blank">bipinelmat@gmail.com</a>> wrote:<br><br><pre>Dear GMX users,<br>I want to calculate the correlated motion between atoms during the md simulation<br>
for that purpose I am using g_covar(the one which is available under <a href="http://www.gromacs.org/Downloads/User_contributions/Other_software" target="_blank">http://www.gromacs.org/Downloads/User_contributions/Other_software</a>)<br>
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 <br>GROMKACS-4.5.3.<br><br></pre>-- <br><font color="#3333ff"><i><font face="arial, helvetica, sans-serif"><div> ---------------------------------<br>Thanks and regards<br></div><div><span style="font-family: arial; font-style: normal;"><i><font face="arial, helvetica, sans-serif">Bipin Singh</font></i></span></div></font></i></font><div> <font color="#3333ff" face="arial, helvetica, sans-serif"><i><br></i></font></div><br> <br>--<br> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br> Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br> Please don't post (un)subscribe requests to the list. Use the<br> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote> <br><br>---------- Forwarded message ----------<br>From: bipin singh <<a href="mailto:bipinelmat@gmail.com">bipinelmat@gmail.com</a>><br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br> Date: Mon, 21 Feb 2011 13:17:48 +0530<br>Subject: Re: [gmx-users] g_covar to calculate correlation of motion<br>Hi,<br>Thanks for your suggestion. <br>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.<br> <br>Choose a group for the least squares fit<br>Opening library file aminoacids.dat<br>WARNING 2 [file aminoacids.dat, line 1]:<br> File aminoacids.dat is empty<br>Group 0 ( System) has 30585 elements<br>Group 1 ( GLU) has 47 elements<br> Group 2 ( HIS) has 86 elements<br>Group 3 ( ASN) has 224 elements<br>Group 4 ( PRO) has 56 elements<br>Group 5 ( VAL) has 272 elements<br>Group 6 ( MET) has 68 elements<br> Group 7 ( GLY) has 168 elements<br>Group 8 ( ILE) has 190 elements<br>Group 9 ( ALA) has 110 elements<br>Group 10 ( SER) has 143 elements<br>Group 11 ( PHE) has 80 elements<br> Group 12 ( LYS) has 242 elements<br>Group 13 ( TYR) has 189 elements<br>Group 14 ( LEU) has 304 elements<br>Group 15 ( GLN) has 102 elements<br>Group 16 ( TRP) has 48 elements<br> Group 17 ( ARG) has 120 elements<br>Group 18 ( ASP) has 108 elements<br>Group 19 ( THR) has 141 elements<br>Group 20 ( SOL) has 27882 elements<br>Group 21 ( CL) has 5 elements<br> <br><br><div class="gmail_quote">On Mon, Feb 21, 2011 at 12:44, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com" target="_blank">tsjerkw@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><p>Hi Bipin,</p><p>Try using a .gro or .pdb file as reference structure (-s). Only .tpr files are version specific.</p><p>Cheers,</p><p>Tsjerk</p><div><br class="webkit-block-placeholder"></div><blockquote type="cite"><div><div></div><div>On Feb 21, 2011 8:05 AM, "bipin singh" <<a href="mailto:bipinelmat@gmail.com" target="_blank">bipinelmat@gmail.com</a>> wrote:<br><br><pre>Dear GMX users,<br>
I want to calculate the correlated motion between atoms during the md simulation<br>
for that purpose I am using g_covar(the one which is available under <a href="http://www.gromacs.org/Downloads/User_contributions/Other_software" target="_blank">http://www.gromacs.org/Downloads/User_contributions/Other_software</a>)<br>
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 <br>GROMKACS-4.5.3.<br><br></pre>-- <br><font color="#3333ff"><i><font face="arial, helvetica, sans-serif"><div> ---------------------------------<br>Thanks and regards<br></div><div><span style="font-family: arial; font-style: normal;"><i><font face="arial, helvetica, sans-serif">Bipin Singh</font></i></span></div></font></i></font><div> <font color="#3333ff" face="arial, helvetica, sans-serif"><i><br></i></font></div><br> <br></div></div>--<br> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br> Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br> Please don't post (un)subscribe requests to the list. Use the<br> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote> <br>--<br> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br> Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br> Please don't post (un)subscribe requests to the list. Use the<br> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote></div><br><br clear="all"><br>-- <br><font color="#3333ff"><i><font face="arial, helvetica, sans-serif"><div> ---------------------------------<br>Thanks and regards<br></div><div><span style="font-family: arial; font-style: normal;"><i><font face="arial, helvetica, sans-serif">Bipin Singh</font></i></span></div></font></i></font><div> <font color="#3333ff" face="arial, helvetica, sans-serif"><i><br></i></font></div><br> <br><br>---------- Forwarded message ----------<br>From: Evelyne Deplazes <<a href="mailto:deplae01@student.uwa.edu.au">deplae01@student.uwa.edu.au</a>><br>To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br> Date: Mon, 21 Feb 2011 15:52:38 +0800<br>Subject: [gmx-users] removing pbc jumps from trajectory<br>Hi <br><br>I have a series of trajectories from a coarse grained simulation (Martini force field) that I ran using gromacs 4.0.4. The system consists of a protein embedded in a POPC bilayer solvated with water. During the simulation the protein (most of time its actually *part* of the protein) jumps across the pb into the neighboring box. I use a series of tcl scripts to analyse my trajectories and for that purpose I need to remove that "period boundary jump" and make the protein "whole" again. <br> <br>I have tried the approach described on the gromacs website <a href="http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions" target="_blank">http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions</a><br> <br>I also other combinations of -whole, -center and -pbc nojump of trjconv, without any luck. Can anyone suggest how I can re-center the protein and remove the pb jump ie make the protein "whole"<br><br>Thanks <br> Evelyne <br><br>-- <br>Evelyne Deplazes<br><br>PhD student <br>Theoretical Chemistry group<br>University of Western Australia <br><br> <br><br>---------- Forwarded message ----------<br>From: XAvier Periole <<a href="mailto:x.periole@rug.nl">x.periole@rug.nl</a>><br>To: "<a href="mailto:deplae01@student.uwa.edu.au">deplae01@student.uwa.edu.au</a>" <<a href="mailto:deplae01@student.uwa.edu.au">deplae01@student.uwa.edu.au</a>>, Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br> Date: Mon, 21 Feb 2011 09:01:54 +0100<br>Subject: Re: [gmx-users] removing pbc jumps from trajectory<br><div bgcolor="#FFFFFF"><div><br></div><div>You have to make sure of two things:</div><div><br></div><div>1- use a reference (gro or tpr) where the molecule is whole! The tpr is prefered since the molecules are defined. </div> <div><br></div><div>2- with such a reference and the option -mol you'll get a trajectory with the protein as a whole. </div><div><br></div><div>On that trajectory you may apply more modifications: </div><div>-nojump with generate a trajectory where the pbc are not applied so you can do msd analysis. Note that thisnis done by default in g_msd. </div> <div>- fitting with only translation removed (equivalent to centering but more stable. Centering works strangely)</div><div><br></div><div>XAvier. </div><div><br>On Feb 21, 2011, at 8:52, Evelyne Deplazes <<a href="mailto:deplae01@student.uwa.edu.au" target="_blank">deplae01@student.uwa.edu.au</a>> wrote:<br> <br></div><div></div><blockquote type="cite"><div>Hi <br><br>I have a series of trajectories from a coarse grained simulation (Martini force field) that I ran using gromacs 4.0.4. The system consists of a protein embedded in a POPC bilayer solvated with water. During the simulation the protein (most of time its actually *part* of the protein) jumps across the pb into the neighboring box. I use a series of tcl scripts to analyse my trajectories and for that purpose I need to remove that "period boundary jump" and make the protein "whole" again. <br> <br>I have tried the approach described on the gromacs website <a href="http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions" target="_blank"></a><a href="http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions" target="_blank">http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions</a><br> <br>I also other combinations of -whole, -center and -pbc nojump of trjconv, without any luck. Can anyone suggest how I can re-center the protein and remove the pb jump ie make the protein "whole"<br><br>Thanks <br> Evelyne <br><br>-- <br>Evelyne Deplazes<br><br>PhD student <br>Theoretical Chemistry group<br>University of Western Australia <br><br> </div></blockquote><blockquote type="cite"><div><span>-- </span><br><span>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank"></a><a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a></span><br> <span><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a></span><br><span>Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!</span><br> <span>Please don't post (un)subscribe requests to the list. Use the </span><br><span>www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.</span><br> <span>Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank"></a><a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a></span></div> </blockquote></div><br>--<br> gmx-users mailing list<br> <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br> Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br></blockquote></div><br><br clear="all"> <br>-- <br>Evelyne Deplazes<br><br>PhD student <br>Theoretical Chemistry group<br>University of Western Australia <br><br> -- <br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists</blockquote></div><br></body></html>