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<body class='hmmessage'><div style="text-align: left;"><br></div>Dear Sir,<br><br>I am sorry I missed the information.<br>The problem was while using grompp.<br>Force field used is g34a1 and operating system is Linux.<br><br>Regards<br><br><br><br><br><hr id="stopSpelling">> Date: Sat, 20 Oct 2007 08:38:19 +0200<br>> From: spoel@xray.bmc.uu.se<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] Using h-angles taking to much time<br>> <br>> harpreet singh wrote:<br>> > <br>> > Dear Sir,<br>> > <br>> > I am running Molecular dynamics simulation. Using other constraints the <br>> > program is running very fast but if I am using constraints = h-angles <br>> > or all-angles the program is taking too much of time (running since last <br>> > 12 hours).<br>> > <br>> > Kindly suggest me that is it the normal behavior of the program or <br>> > something went wrong with my data.<br>> <br>> maybe, maybe not. it would have been helpful if you specified that the <br>> problem was in grompp.<br>> <br>> which force field are you using?<br>> which OS and compiler?<br>> <br>> > <br>> > Regards<br>> > <br>> > <br>> > <br>> > <br>> > <br>> > <br>> > <br>> > <br>> > <br>> > <br>> > <br>> > -nice int 0 Set the nicelevel<br>> > -[no]v bool yes Be loud and noisy<br>> > -time real -1 Take frame at or first after this time.<br>> > -np int 1 Generate statusfile for # nodes<br>> > -[no]shuffle bool no Shuffle molecules over nodes<br>> > -[no]sort bool no Sort molecules according to X coordinate<br>> > -[no]rmvsbds bool yes Remove constant bonded interactions with vi<br>> > sites<br>> > -load string Releative load capacity of each node on a<br>> > parallel machine. Be sure to use quotes aro<br>> > the string, which should contain a number f<br>> > each node<br>> > -maxwarn int 10 Number of warnings after which input proces<br>> > stops<br>> > -[no]check14 bool no Remove 1-4 interactions without Van der Waa<br>> > -[no]renum bool yes Renumber atomtypes and minimize number of<br>> > atomtypes<br>> > <br>> > creating statusfile for 1 node...<br>> > <br>> > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.16#<br>> > checking input for internal consistency...<br>> > calling /usr/bin/cpp...<br>> > processing topology...<br>> > Generated 279 of the 1225 non-bonded parameter combinations<br>> > Excluding 3 bonded neighbours for Protein_A 1<br>> > turning all bonds and H angles into constraints...<br>> > <br>> > <br>> > Help yourself to FREE treats served up daily at the Messenger Café. Stop <br>> > by today! <br>> > <http://www.cafemessenger.com/info/info_sweetstuff2.html?ocid=TXT_TAGLM_OctWLtagline><br>> > <br>> > <br>> > ------------------------------------------------------------------------<br>> > <br>> > _______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php<br>> <br>> <br>> -- <br>> David van der Spoel, Ph.D.<br>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<br>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.<br>> spoel@xray.bmc.uu.se spoel@gromacs.org http://folding.bmc.uu.se<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php<br><br /><hr />Boo! Scare away worms, viruses and so much more! Try Windows Live OneCare! <a href='http://onecare.live.com/standard/en-us/purchase/trial.aspx?s_cid=wl_hotmailnews' target='_new'>Try now!</a></body>
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