I am new to gromacs and need help regarding interpratation of the results...where to look for<br><b><i>gmx-users-request@gromacs.org</i></b> wrote:<blockquote class="replbq" style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"> Send gmx-users mailing list submissions to<br> gmx-users@gromacs.org<br><br>To subscribe or unsubscribe via the World Wide Web, visit<br> http://www.gromacs.org/mailman/listinfo/gmx-users<br>or, via email, send a message with subject or body 'help' to<br> gmx-users-request@gromacs.org<br><br>You can reach the person managing the list at<br> gmx-users-owner@gromacs.org<br><br>When replying, please edit your Subject line so it is more specific<br>than "Re: Contents of gmx-users digest..."<br><br><br>Today's Topics:<br><br> 1. Re: indexing atoms (Erik Marklund)<br> 2. rdf (Claus Valka)<br> 3. potential oxiredution (Elias santos)<br> 4. Re: potential oxiredution (Mark Abraham)<br> 5. Re: problem in compiling
g_velacc again under gromacs<br> (Mark Abraham)<br> 6. Re: problem in compiling g_velacc again under gromacs (Qiao Baofu)<br> 7. Re: problem in compiling g_velacc again under gromacs (Qiao Baofu)<br> 8. pulldim vectors in pull code (Mauricio Sica)<br><br><br>----------------------------------------------------------------------<br><br>Message: 1<br>Date: Tue, 31 Oct 2006 09:39:01 +0100<br>From: Erik Marklund <erikm @xray.bmc.uu.se=""><br>Subject: Re: [gmx-users] indexing atoms<br>To: Discussion list for GROMACS users <gmx-users @gromacs.org=""><br>Message-ID: <1162283942.28794.6.camel@jorn.bmc.uu.se><br>Content-Type: text/plain; charset=utf-8<br><br>You can sort the atoms according to position using grompp, but I don't<br>think that's the easiest solution. I would use awk or something along<br>those lines, to find all atoms within z=[4 5] nm and remove everything<br>except the indexes. Put a bracketed name on top of it all and violà , you<br>have
turned them into an index group.<br><br>/Erik<br><br>On Tue, 2006-10-31 at 00:37 -0600, toma0052 wrote:<br>> Hello,<br>> I have a question regarding indexing atoms for use with<br>> non-equilibrium MD. The manual says that I can select atoms by number or<br>> type; I was wondering if there is a way in Gromacs to index atoms by<br>> position with the simulation box. I am looking to add an acceleration to<br>> the solvent, but not the entire solvent. Is there a way that I can specify<br>> solvent molecules within a certain coordinate ie. a z-position from 4nm to<br>> 5nm with the simulation box being 6nm in height? I am looking to<br>> accelerate solvent molecules near a lipid bilayer, but if a particular<br>> solvent molecule diffuses too far from the bilayer, I no longer want it to<br>> keep its fixed acceleration. Is there any way that indexing by coordinates<br>> is possible?<br>> <br>> Thank you,<br>> Mike
Tomasini<br>> <br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<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/mailing_lists/users.php<br>-- <br>Erik Marklund, PhD Student, Molecular Biopcysics group,<br>Dept. of Cell and Molecular Biology, Uppsala University.<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: +46 18 471 4537 fax: +46 18 511 755<br>erikm@xray.bmc.uu.se<br><br><br><br>------------------------------<br><br>Message: 2<br>Date: Tue, 31 Oct 2006 13:16:27 +0100 (CET)<br>From: Claus Valka <lastexile7gr @yahoo.de=""><br>Subject: [gmx-users] rdf<br>To: gmx-users@gromacs.org<br>Message-ID: <20061031121627.71473.qmail@web26602.mail.ukl.yahoo.com><br>Content-Type: text/plain;
charset=iso-8859-1<br><br>Title : radial distribution function, 31.10.06<br><br> Hello, <br> <br> I am a new user of Gromacs (just started my<br>Phd), and<br> I'm trying to calculate the partial radial<br>distibution functions <br> for a system of polymer chains.<br> <br> In the topology file the system is described as <br> <br> 1) 2 different types of chains <br> (essentially similar in chemistry, with<br>different helicity)<br> <br> 2) C, H, CH3 atom types in each chain (3<br>different bead types)<br> <br> I would like to calculate the rdfs for the<br>partial correlations<br> corresponding to pairs of the type<br> <br> a) C - all <br> b) C - C<br> c) C - CH3<br> d) C - H<br> e) CH3 - H<br> <br> for <br> <br> A) intra-pairs (same chain) <br> B) inter-pairs (different chains)<br> C) any pair<br> <br> i.e., pair
correlations A[a,b,c,d,e], B[...] and<br>so on,<br> over all chains in the system. <br> <br> In the manual it is said that an index file is<br>needed <br> How could I describe the groups in index file so<br>as to make these<br> calculations in an efficient way? Is there any<br>easy way to describe<br> various kind of desired 'pairing correlations'<br>in Gromacs?<br> <br> Any help would be appreciated,<br> Nick<br><br><br> <br>___________________________________________________________ <br>Telefonate ohne weitere Kosten vom PC zum PC: http://messenger.yahoo.de<br><br><br>------------------------------<br><br>Message: 3<br>Date: Tue, 31 Oct 2006 10:56:29 -0200<br>From: "Elias santos" <silvasantosster @gmail.com=""><br>Subject: [gmx-users] potential oxiredution<br>To: gmx-users <gmx-users @gromacs.org=""><br>Message-ID:<br> <97baf6380610310456v6378b0dfj15ea88bdcef038fa@mail.gmail.com><br>Content-Type: text/plain;
charset="iso-8859-1"<br><br>Hi!!<br> I have a question for you...<br>Some way to calculate the oxiredution potential (ORP) using the Gromacs<br>package?<br><br>Elias<br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20061031/fef95973/attachment-0001.html<br><br>------------------------------<br><br>Message: 4<br>Date: Wed, 01 Nov 2006 00:10:34 +1100<br>From: Mark Abraham <Mark.Abraham @anu.edu.au=""><br>Subject: Re: [gmx-users] potential oxiredution<br>To: Discussion list for GROMACS users <gmx-users @gromacs.org=""><br>Message-ID: <45474B4A.6080206@anu.edu.au><br>Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br><br>Elias santos wrote:<br><br>> Some way to calculate the oxiredution potential (ORP) using the Gromacs <br>> package?<br><br>No, since you can't simulate a system with MD that's large enough that <br>such a bulk observable would be at all
meaningful - and even then you'd <br>get out the answer you put in by choosing the solutes.<br><br>Mark<br><br><br>------------------------------<br><br>Message: 5<br>Date: Wed, 01 Nov 2006 00:19:05 +1100<br>From: Mark Abraham <Mark.Abraham @anu.edu.au=""><br>Subject: Re: [gmx-users] problem in compiling g_velacc again under<br> gromacs<br>To: Discussion list for GROMACS users <gmx-users @gromacs.org=""><br>Message-ID: <45474D49.9000907@anu.edu.au><br>Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br><br>Qiao Baofu wrote:<br>> Hi all,<br>> <br>> I want to comile the g_velacc again. I copy the original gmx_velacc.c <br>> and autocorr.c into a new directory, and then comile the gmx_velacc.c, <br>> but it gives the following complains, and then exits. (I didn't change <br>> anything in the two files!!) How to solve it? Thanks a lot.<br><br>Does it work if you do it in the same directory? That's got to be
cleaner...<br><br>Mark<br><br><br>------------------------------<br><br>Message: 6<br>Date: Tue, 31 Oct 2006 15:07:26 +0100<br>From: "Qiao Baofu" <qiaobf @gmail.com=""><br>Subject: Re: [gmx-users] problem in compiling g_velacc again under<br> gromacs<br>To: "Discussion list for GROMACS users" <gmx-users @gromacs.org=""><br>Message-ID:<br> <6a91f07b0610310607r1c6b6c93lc042a1f04df1e736@mail.gmail.com><br>Content-Type: text/plain; charset="iso-8859-1"<br><br>Hi,<br><br>I compile it again in the source folder ~/src/tool/ and the installation<br>folder ~/gromacs/bin. It give the same complains.<br><br>What can I do?<br><br><br>2006/10/31, Mark Abraham <Mark.Abraham @anu.edu.au="">:<br>><br>> Qiao Baofu wrote:<br>> > Hi all,<br>> ><br>> > I want to comile the g_velacc again. I copy the original gmx_velacc.c<br>> > and autocorr.c into a new directory, and then comile the gmx_velacc.c,<br>> > but it gives the following complains, and
then exits. (I didn't change<br>> > anything in the two files!!) How to solve it? Thanks a lot.<br>><br>> Does it work if you do it in the same directory? That's got to be<br>> cleaner...<br>><br>> Mark<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<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/mailing_lists/users.php<br>><br><br><br><br>-- <br>Sincerely yours,<br>**********************************************<br>Baofu Qiao, PhD<br>Frankfurt Institute for Advanced Studies<br>Max-von-Laue-Str. 1<br>60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529<br>**********************************************<br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL:
http://www.gromacs.org/pipermail/gmx-users/attachments/20061031/472f21b5/attachment-0001.html<br><br>------------------------------<br><br>Message: 7<br>Date: Tue, 31 Oct 2006 16:19:14 +0100<br>From: "Qiao Baofu" <qiaobf @gmail.com=""><br>Subject: Re: [gmx-users] problem in compiling g_velacc again under<br> gromacs<br>To: "Discussion list for GROMACS users" <gmx-users @gromacs.org=""><br>Message-ID:<br> <6a91f07b0610310719ne37ed8x5684ea3327cc2426@mail.gmail.com><br>Content-Type: text/plain; charset="iso-8859-1"<br><br>I think the problem is because I compile Gromacs under 64-bite model. the<br>g_velacc.c can not be recognized under 64 bite model.<br><br>But when I compile it under 32-bite it gives the following complains. On the<br>other hand I am not sure whether a file (which is ok under 32-bite system )<br>can be copied to 64-bite system.<br><br>/usr/bin/ld: skipping incompatible /home/fias/qiao/Gromacs//lib/libmd.a when<br>searching for -lmd<br>/usr/bin/ld:
skipping incompatible /home/fias/qiao/Gromacs//lib/libmd.a when<br>searching for -lmd<br>/usr/bin/ld: cannot find -lmd<br>collect2: ld returned 1 exit status<br><br><br><br><br>2006/10/31, Qiao Baofu <qiaobf @gmail.com="">:<br>><br>> Hi,<br>><br>> I compile it again in the source folder ~/src/tool/ and the installation<br>> folder ~/gromacs/bin. It give the same complains.<br>><br>> What can I do?<br>><br>><br>> 2006/10/31, Mark Abraham < Mark.Abraham@anu.edu.au>:<br>> ><br>> > Qiao Baofu wrote:<br>> > > Hi all,<br>> > ><br>> > > I want to comile the g_velacc again. I copy the original gmx_velacc.c<br>> > > and autocorr.c into a new directory, and then comile the gmx_velacc.c,<br>> > > but it gives the following complains, and then exits. (I didn't change<br>> ><br>> > > anything in the two files!!) How to solve it? Thanks a lot.<br>> ><br>> > Does
it work if you do it in the same directory? That's got to be<br>> > cleaner...<br>> ><br>> > Mark<br>> > _______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://www.gromacs.org/mailman/listinfo/gmx-users<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/mailing_lists/users.php<br>> ><br>><br>><br>><br>> --<br>> Sincerely yours,<br>> **********************************************<br>> Baofu Qiao, PhD<br>> Frankfurt Institute for Advanced Studies<br>> Max-von-Laue-Str. 1<br>> 60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529<br>> **********************************************<br>><br><br><br><br>-- <br>Sincerely yours,<br>**********************************************<br>Baofu Qiao,
PhD<br>Frankfurt Institute for Advanced Studies<br>Max-von-Laue-Str. 1<br>60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529<br>**********************************************<br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20061031/0c495e5d/attachment-0001.html<br><br>------------------------------<br><br>Message: 8<br>Date: Tue, 31 Oct 2006 17:21:57 -0300<br>From: "Mauricio Sica" <msica @unq.edu.ar=""><br>Subject: [gmx-users] pulldim vectors in pull code<br>To: <gmx-users @gromacs.org=""><br>Message-ID: <003d01c6fd2a$3f3b9140$3800020a@CYT032><br>Content-Type: text/plain; charset="iso-8859-1"<br><br>Dear users<br><br>I have the following problem. I'm using the pull code to bring near two<br>peptides initially 2.7 nm apart. The problem is that the run crush when I<br>choose "pulldim = Y Y Y or Y N N ", but doesn't when I use N N Y. I can't<br>understand what's
wrong.<br>Maybe I don't understand what's the vector I am choosing in pulldim option.<br>I know it is the x, y or z axis. But is it a box vector? A distance vector?<br>In this case, why x, y and z if distance is one-dimensional? It was not<br>clear (at least for me) in the manuals (3.2 or<br>3.3)<br><br>Thanks in advance<br><br>My pull.ppa is<br>---------------<br>verbose = no<br>Skip steps = 10<br>runtype = constraint<br>ngroups = 1<br>group_1 = G1<br>reference_group = GR<br>reftype = com_t0<br>reflag = 1<br>pulldim = Y Y Y or N N Y or Y N N ; the three options I used. Only N N Y<br>worked<br>constraint_direction = 0.0 0.0 0.0<br>constraint_distance1 =<br>constraint_rate1 = -0.00007<br>constraint_tolerance = 0.1<br><br><br>Dr. Mauricio Pablo Sica<br>Laboratorio de Expresión y Plegado Proteico (LEPP)<br>Dpto. de Ciencia y Tecnología<br>Universidad Nacional de Quilmes (UNQ)<br>R. Saenz Peña 352 (B1876BXF)<br>Bernal, Pcia de Buenos
Aires<br>Argentina<br><br><br><br><br><br>------------------------------<br><br>_______________________________________________<br>gmx-users mailing list<br>gmx-users@gromacs.org<br>http://www.gromacs.org/mailman/listinfo/gmx-users<br><br><br>End of gmx-users Digest, Vol 30, Issue 75<br>*****************************************<br></gmx-users></msica></qiaobf></gmx-users></qiaobf></Mark.Abraham></gmx-users></qiaobf></gmx-users></Mark.Abraham></gmx-users></Mark.Abraham></gmx-users></silvasantosster></lastexile7gr></gmx-users></erikm></blockquote><br><p> 
        
        
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