<html><body><div style="color:#000; background-color:#fff; font-family:bookman old style, new york, times, serif;font-size:14pt"><div><span>Hi Tsjerk, <br></span></div><div><span><br></span></div><div><span>I have a good news!!! That was corrected!!!</span><br></div><div><br></div><div>Thank you very much from your help.</div><div><br></div><div>Best Regards</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 size="2" face="Arial"> <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> Wednesday, January 11, 2012 2:12 PM<br> <b><span
style="font-weight: bold;">Subject:</span></b> Re: Fw: [gmx-users] trjconv in martini<br> </font> <br>
Hi Sara,<br><br>You have to understand what is happening. You don't have a static<br>system. Using -pbc nojump, in combination with <a target="_blank" href="http://xtcrev.py">xtcrev.py</a> may help you<br>get a view in which the molecules seem to settle on a specific view or<br>clustering of your systems, in which you have the micelles. But they<br>will be dispersed before, and maybe after. If you use -pbc cluster,<br>the same thing will happen. trjconv will try to form clusters for<br>every frame, but in some frames there are no clear cut clusters.<br>Usually you can't have it all, and usually you will have to try<br>several things. First of all, you have to think of the goal. Is it for<br>visualization, or is it for further analysis. The needs for these two<br>are usually different.<br><br>Cheers,<br><br>Tsjerk<br><br>On Wed, Jan 11, 2012 at 11:32 AM, mohammad agha <<a ymailto="mailto:mra_bu@yahoo.com"
href="mailto:mra_bu@yahoo.com">mra_bu@yahoo.com</a>> wrote:<br>> Hi Tsjerk,<br>><br>> Thank you very very much from your help about xtcrev.py script, I did it<br>> till end according to you said me before, but unfortunately my first problem<br>> about view of 2 micelles was not solved and monomers are dispersed during<br>> simulation!!! I don't know why!!!<br>> You helped me very much and thank you very much but may I ask you any<br>> suggestion about my problem, please?<br>><br>> Best Regards<br>> Sara<br>><br>><br>> ________________________________<br>> rom: Tsjerk Wassenaar <<a ymailto="mailto:tsjerkw@gmail.com" href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>><br>> To: mohammad agha <<a ymailto="mailto:mra_bu@yahoo.com" href="mailto:mra_bu@yahoo.com">mra_bu@yahoo.com</a>>; Discussion list for GROMACS users<br>> <<a ymailto="mailto:gmx-users@gromacs.org"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> Sent: Wednesday, January 11, 2012 1:38 PM<br>><br>> Subject: Re: Fw: [gmx-users] trjconv in martini<br>><br>> Hi Sara,<br>><br>> If you give two arguments, it shouldn't do that. './xtcrev.py<br>> input.xtc output.xtc' should work fine. Of course I could've clogged<br>> the script with checking the number of input files and such, and maybe<br>> I will later, but for now it's just a nifty hack :p<br>><br>> Cheers,<br>><br>> Tsjerk<br>><br>> On Wed, Jan 11, 2012 at 11:05 AM, mohammad agha <<a ymailto="mailto:mra_bu@yahoo.com" href="mailto:mra_bu@yahoo.com">mra_bu@yahoo.com</a>> wrote:<br>>> Hi Tsjerk,<br>>><br>>> Thank you very much from your reply. Yes, you're right, I corrected that,<br>>> but now it gave me this error:<br>>><br>>> Traceback (most recent call last):<br>>> File
"./xtcrev.py", line 68, in <module><br>>> o = open(sys.argv[2],"w")<br>>> IndexError: list index out of range<br>>><br>>> May I ask you to help me, please?<br>>><br>>> Best Regards<br>>> Sara<br>>> ________________________________<br>>> From: Tsjerk Wassenaar <<a ymailto="mailto:tsjerkw@gmail.com" href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>><br>>> To: mohammad agha <<a ymailto="mailto:mra_bu@yahoo.com" href="mailto:mra_bu@yahoo.com">mra_bu@yahoo.com</a>>; Discussion list for GROMACS users<br>>> <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>>> Sent: Wednesday, January 11, 2012 12:54 PM<br>>><br>>> Subject: Re: Fw: [gmx-users] trjconv in martini<br>>><br>>> Hi Sara,<br>>><br>>> That can only happen if the input file is
empty.<br>>> But I now see that the output file should be given as second argument,<br>>> so it should be<br>>><br>>> ./xtcrev.py input.xtc output.xtc<br>>><br>>> rather than<br>>><br>>> ./xtcrev.py input.xtc > output.xtc<br>>><br>>> The latter will actually result in an empty xtc file. Maybe that's the<br>>> cause of the problem? Sorry about that.<br>>><br>>> Cheers,<br>>><br>>> Tsjerk<br>>><br>>> On Tue, Jan 10, 2012 at 6:38 PM, mohammad agha <<a ymailto="mailto:mra_bu@yahoo.com" href="mailto:mra_bu@yahoo.com">mra_bu@yahoo.com</a>> wrote:<br>>>> Hi Tsjerk,<br>>>><br>>>> I know that my question is silly but please help me.<br>>>> I installed python2.5 on my system, then I ran "./xtcrev.py 1a.xtc ><br>>>> 1a-rev.xtc" but it gave me following error:<br>>>><br>>>> Traceback (most
recent call last):<br>>>> File "./xtcrev.py", line 54, in <module><br>>>> n = 92 + i(f.read(84)[-4:]) # Size of frame in bytes<br>>>> File "./xtcrev.py", line 24, in i<br>>>><br>>>> def i(x): return sum([ord(x[j])<<(24-j*8) for j in range(4)])<br>>>> IndexError: string index out of range<br>>>><br>>>> I know that j is out of range but I don't know that what should I do<br>>>> exactly?<br>>>> May I ask you to help me, Please?<br>>>><br>>>> Best Regards<br>>>> Sara<br>>>> ________________________________<br>>>> From: Tsjerk Wassenaar <<a ymailto="mailto:tsjerkw@gmail.com" href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>><br>>>> To: mohammad agha <<a ymailto="mailto:mra_bu@yahoo.com"
href="mailto:mra_bu@yahoo.com">mra_bu@yahoo.com</a>>; Discussion list for GROMACS users<br>>>> <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>>>> Sent: Saturday, December 31, 2011 3:41 PM<br>>>><br>>>> Subject: Re: Fw: [gmx-users] trjconv in martini<br>>>><br>>>> Hi Sara,<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>>>> That should be -e 199999 :) But you can also use -e 200000. Probably<br>>>> that is better. I first thought it'd be better to avoid a double<br>>>> frame, but since trjcat is used to combine the parts again, it doesn't<br>>>> matter.<br>>>><br>>>> Good luck,<br>>>><br>>>>
Tsjerk<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>>>><br>>>> --<br>>>> gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" 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<br>>>> <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 ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">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>>><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>>><br>>> --<br>>> gmx-users mailing list <a
ymailto="mailto:gmx-users@gromacs.org" 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<br>>> <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 ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">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>><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>><br>> --<br>> gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" 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<br>> <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 ymailto="mailto:gmx-users-request@gromacs.org"
href="mailto:gmx-users-request@gromacs.org">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><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></body></html>