<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV>Dear Justin</DIV>
<DIV>many thanks for your email and your comments.</DIV>
<DIV> </DIV>
<DIV>I found aminoacids.dat in the following pat</DIV>
<DIV><BR><STRONG>/apps/gromacs/4.0.5/share/gromacs/top</STRONG></DIV>
<DIV>I connect to imerial college via vpn. they have installed several gromacs versions.</DIV>
<DIV>I only write</DIV>
<DIV><STRONG>module load mpi</STRONG> and then</DIV>
<DIV><STRONG>module load gromacs</STRONG></DIV>
<DIV>and then the gromacs commands become active.</DIV>
<DIV>-------</DIV>
<DIV>the g_msd_mpi command worked and now I have msd.xvg file and I plotted it using gnuplot with this command:</DIV>
<DIV>gnuplot "msd.xvg" u 1:2 w l</DIV>
<DIV>now pls let me know how can I save this plot? I have written about that but I am confused.</DIV>
<DIV> </DIV>
<DIV>Thanks for your time</DIV>
<DIV>Best regards</DIV>
<DIV>Delara</DIV>
<DIV><STRONG><BR></STRONG><BR><BR><BR>--- On <B>Wed, 12/22/10, Justin A. Lemkul <I><jalemkul@vt.edu></I></B> wrote:<BR></DIV>
<BLOCKQUOTE style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: rgb(16,16,255) 2px solid"><BR>From: Justin A. Lemkul <jalemkul@vt.edu><BR>Subject: Re: [gmx-users] location of aminoacids.dat<BR>To: "Gromacs Users' List" <gmx-users@gromacs.org><BR>Date: Wednesday, December 22, 2010, 5:00 PM<BR><BR>
<DIV class=plainMail><BR>First, please start a new thread if you are asking a new question. Hijacking an existing thread confuses the archive and will likely get your question ignored by anyone not interested in reading about Buckingham potentials. I have changed the subject line appropriately.<BR><BR>See comments below.<BR><BR>delara aghaie wrote:<BR>> Dear Justin<BR>> I hope all is well with you. I have faced a problem. I connect to imperial college london from my conunty to do the simulations. Today I faced an strange problem.<BR>> every command wich I want to use for ex: g_msd_mpi or make_ndx_mpi<BR>> I get this fatal error:<BR>> *Fatal error:<BR>> Library file aminoacids.dat not found in current dir nor in default directories.<BR>> (You can set the directories to search with the GMXLIB path variable)*<BR>> It is strange because my system is DPPC monolayer and does not have nothing to do with proteins
!!!<BR>> <BR><BR>That doesn't matter. Certain input files are required by certain Gromacs tools. In all likelihood, you simply haven't set up your environment properly, but I'm not sure how that's possible.<BR><BR>What version of Gromacs are you using? How was it installed? Are the Gromacs executables included in your $PATH, or do you have to find them manually in order to use them (i.e., do you run /path/to/gromacs/bin/grompp or just grompp)?<BR><BR>Also note that there is no value in compiling the entire Gromacs suite with an MPI compiler. I've seen that cause weird behavior before, but I doubt it's necessarily related here. The only MPI-aware program is mdrun.<BR><BR>-Justin<BR><BR>> your help would be greatly appreciated/<BR>> *Best regards*<BR>> *Delara*<BR>> *<BR>> *<BR>> <BR>> --- On *Wed, 12/22/10, Justin A. Lemkul /<<A
href="http://us.mc1301.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu" ymailto="mailto:jalemkul@vt.edu">jalemkul@vt.edu</A>>/* wrote:<BR>> <BR>> <BR>> From: Justin A. Lemkul <<A href="http://us.mc1301.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu" ymailto="mailto:jalemkul@vt.edu">jalemkul@vt.edu</A>><BR>> Subject: Re: [gmx-users] buckingham potentials<BR>> To: "Gromacs Users' List" <<A href="http://us.mc1301.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A>><BR>> Date: Wednesday, December 22, 2010, 8:04 AM<BR>> <BR>> <BR>> <BR>> sreelakshmi ramesh wrote:<BR>> > Dear justin,<BR>> > I have no clues about
rewriting a force field<BR>> so i think i can t proceed with this anymore.<BR>> ><BR>> > thanks a lot for your patient reply.<BR>> <BR>> For the future, you will waste a lot less time (your own, and that<BR>> of those who are trying to help you) if you provide a clear, concise<BR>> statement of what you hope to accomplish in your very first post. You began this adventure seeking help on how to (generically) use<BR>> Buckingham potentials. What you should have asked was how to use<BR>> Buckingham potentials within the Gromos force field. Then, instead<BR>> of swapping ten emails, you would have received your answer in one.<BR>> <BR>> -Justin<BR>>
<BR>> -- ========================================<BR>> <BR>> Justin A. Lemkul<BR>> Ph.D. Candidate<BR>> ICTAS Doctoral Scholar<BR>> MILES-IGERT Trainee<BR>> Department of Biochemistry<BR>> Virginia Tech<BR>> Blacksburg, VA<BR>> jalemkul[at]vt.edu | (540) 231-9080<BR>> <A href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target=_blank>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</A><BR>> <BR>> ========================================<BR>> -- gmx-users mailing list <A href="http://us.mc1301.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org"
ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>> <<A href="http://us.mc1301.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" target=_blank>http://us.mc1301.mail.yahoo.com/mc/compose?to=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 www<BR>> interface or send it to <A href="http://us.mc1301.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org"
ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A><BR>> <<A href="http://us.mc1301.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org" target=_blank>http://us.mc1301.mail.yahoo.com/mc/compose?to=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><BR>Justin A. Lemkul<BR>Ph.D. Candidate<BR>ICTAS Doctoral Scholar<BR>MILES-IGERT Trainee<BR>Department of Biochemistry<BR>Virginia Tech<BR>Blacksburg, VA<BR>jalemkul[at]vt.edu | (540) 231-9080<BR><A href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target=_blank>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</A><BR><BR>========================================<BR>-- gmx-users mailing list
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