<html><body><div style="color:#000; background-color:#fff; font-family:bookman old style, new york, times, serif;font-size:14pt"><div><span></span></div><div><br></div> <div style="font-family: bookman old style, new york, times, serif; font-size: 14pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <font face="Arial" size="2"> ----- Forwarded Message -----<br> <b><span style="font-weight:bold;">From:</span></b> mohammad agha <mra_bu@yahoo.com><br> <b><span style="font-weight: bold;">To:</span></b> Tsjerk Wassenaar <tsjerkw@gmail.com> <br> <b><span style="font-weight: bold;">Sent:</span></b> Friday, December 30, 2011 3:16 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] trjconv in martini<br> </font> <br>
<div id="yiv1311685746"><div><div style="color:#000;background-color:#fff;font-family:bookman old style, new york, times, serif;font-size:14pt;"><div>Hi Tsjerk,</div><div><br></div><div>Thank you very much from your reply, I have a problem about ./xtcrev.py 1a.xtc > 1a-rev.xtc</div>I did ./xtcrev.py 1a.xtc > 1a-rev.xtc but it answered me:<div> from: can't read /var/mail/struct<br>./xtcrev.py: line 21: import: command not found<br>./xtcrev.py: line 22: import: command not found<br>./xtcrev.py: line 24: syntax error near unexpected token `('<br>./xtcrev.py: line 24: `def i(x): return sum([ord(x[j])<<(24-j*8) for j in range(4)])'<br></div><div>May I ask you to help me?</div><div><br></div><div>Best Regards <br></div><div>Sara<br></div> <div style="font-family:bookman old style, new york, times, serif;font-size:14pt;"> <div style="font-family:times new roman, new york, times, serif;font-size:12pt;"> <font face="Arial" size="2"> <hr size="1">
<b><span style="font-weight:bold;">From:</span></b> Tsjerk Wassenaar <tsjerkw@gmail.com><br> <b><span style="font-weight:bold;">To:</span></b> mohammad agha <mra_bu@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight:bold;">Sent:</span></b> Friday, December 30, 2011 3:01 PM<br> <b><span style="font-weight:bold;">Subject:</span></b> Re: [gmx-users] trjconv in martini<br> </font> <br>
Hi Sara,<br><br>Assuming you have saved the script <a rel="nofollow" target="_blank" href="http://xtcrev.py">xtcrev.py</a>:<br><br># Get a clustered reference frame<br>trjconv -s md.tpr -f md.trr -o cluster.gro -pbc cluster -dump 200000<br><br># Extract the first part of the trajectory<br>trjconv -s md.tpr -f md.trr -n index.ndx -o 1a.xtc -e 19999<br><br># Reverse it<br>./xtcrev.py 1a.xtc > 1a-rev.xtc<br><br># Remove jumps<br>trjconv -s cluster.gro -f 1a-rev.xtc -o 1a-rev-clus.xtc -pbc nojump<br><br># Reverse it again<br>./xtcrev.py 1a-rev-clus.xtc > 1a-clus.xtc<br><br># Extract the second part of the trajectory<br>trjconv -s md.tpr -f md.trr -o 1b.xtc -b 200000<br><br># Remove jumps<br>trjconv -s cluster.gro -f md.trr -pbc nojump -o 1b-clus.xtc<br><br># Put the two together<br>trjcat -f 1a-clus.xtc 1b-clus.xtc -o clustered.xtc<br><br># Hope it helps<br><br># Tsjerk<br><br><br><br>On Fri, Dec 30, 2011 at 12:01 PM, mohammad agha <<a
rel="nofollow" ymailto="mailto:mra_bu@yahoo.com" target="_blank" href="mailto:mra_bu@yahoo.com">mra_bu@yahoo.com</a>> wrote:<br>> Dear gromacs users,<br>><br>> At the first I thank from Tsjerk and Mark because of their answers to me but<br>> unfortunately I don't understand that where is my mistake, still?<br>> I work with MARTINI coarse-grained and I have a problem after -pbc nojump!<br>> My simulation lasts 600 ns and 2 micelles are created from 200 ns and remain<br>> during 400 ns, then my micelles isn't formed at the end of the trajectory.<br>> My commands are:<br>> 1- trjconv -f md.trr -s md.tpr -n index.ndx -e 600000 -pbc cluster -o 1.gro<br>> In this step I viewed 2 micelles from 200 ns to 600 ns by ngmx -f 1.gro -s<br>> md.tpr, so I have 2 micelles and -pbc cluster works me well and has been<br>> removed box boundaries from my system but I saw very jumps in my system.<br>> Okay?<br>> 2- grompp
-f md.mdp -c 1.gro -o 1.tpr -n
index.ndx<br>> 3- trjconv -f 1.gro -s 1.tpr -o 2.xtc -pbc nojump<br>> After this step, had been removed jumps but I didn't see 2 micelles in 200<br>> ns, I saw that my monomers were collected as groups in the different places.<br>> (This is bad and I don't know where is my mistake and what should I do to<br>> solve my problem!)<br>> After this, to solve my problem, I did:<br>> 4- trjconv -f 2.xtc -s 1.tpr -o 3.xtc -pbc mol<br>> In this step, I viewed 2 micelles from 200 ns to 600 ns and had been removed<br>> jumps but existed boundaries of box, means my micelles that leaves a<br>> simulation box by, say, the right-hand face, then enters the simulation box<br>> by the left-hand face.<br>> May I know can I start analysis of my system with 3.xtc? Is it good? If it<br>> isn't good, Please help me for this problem with nojump.<br>><br>> Thank you very much in advance<br>> Best Regards<br>>
Sara<br>><br>> --<br>> gmx-users mailing list <a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at<br>> <a rel="nofollow" target="_blank" href="http://www.gromacs.org/Support/Mailing_Lists/Search">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 rel="nofollow" ymailto="mailto:gmx-users-request@gromacs.org" target="_blank" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br><br><br><br>-- <br>Tsjerk A. Wassenaar, Ph.D.<br><br>post-doctoral researcher<br>Molecular Dynamics Group<br>* Groningen Institute for Biomolecular
Research and Biotechnology<br>* Zernike Institute for Advanced
Materials<br>University of Groningen<br>The Netherlands<br><br><br> </div> </div> </div></div></div><br><br> </div> </div> </div></body></html>