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Yes I was using ffgmx. I tried to use oplsaa but it didn't work. I am using gromacs 3.3.1 and it looks like it doesn't have n2t file beside ffgmx.<div>How can i use oplsaa in gromacs 3.3.1</div><div><br></div><div><br><br>> Date: Mon, 8 Mar 2010 18:34:23 -0500<br>> Subject: Re: [gmx-users] large number of molecules<br>> From: ostueker@gmail.com<br>> To: jalemkul@vt.edu; gmx-users@gromacs.org<br>> CC: <br>> <br>> Hi Karim,<br>> <br>> On Mon, Mar 8, 2010 at 18:11, Justin A. Lemkul <jalemkul@vt.edu> wrote:<br>> ><br>> ><br>> > ksm tprk wrote:<br>> >><br>> >> My mdp file is what http://cs86.com/CNSE/SWNT.htm has. I used nose-hoover<br>> >> for Tcouple.<br>> >> and the beginning of mdp code looks like:<br>> >><br>> ><br>> > Partial information is useless. Post the whole .mdp file; there are plenty<br>> > of parameters that can be set incorrectly or inconsistently.<br>> <br>> In addition to Justin, you haven't told us even which forcefield you are using.<br>> I hope it's not ffgmx as it is in the reference you gave us. Search<br>> the Archive and the Gromacs wiki for reasons not to use ffgmx.<br>> <br>> Oliver<br>> <br>> > -Justin<br>> ><br>> >> ; RUN CONTROL PARAMETERS<br>> >> integrator = md<br>> >> ; Start time and timestep in ps<br>> >> tinit = 0<br>> >> dt = 0.0005<br>> >> nsteps = 10000000<br>> >> ; For exact run continuation or redoing part of a run<br>> >> init_step = 0<br>> >> ; mode for center of mass motion removal<br>> >> comm-mode = Angular<br>> >> ; number of steps for center of mass motion removal<br>> >> nstcomm = 1<br>> >> ; group(s) for center of mass motion removal<br>> >> comm-grps =<br>> >><br>> >><br>> >> I used gromacs 3.3.3 and in the vacuum. I applied the heat first around 10<br>> >> layers.<br>> >> after I finished my simulation and look at the edr file, the result<br>> >> temperatures are higher than what I gave. It looks like it generates heat by<br>> >> it self.<br>> >> But when I do same simulation with less molecules such as 6000, it looks<br>> >> fine.<br>> >><br>> >><br>> >><br>> >><br>> >> ------------------------------------------------------------------------<br>> >> Date: Tue, 9 Mar 2010 08:57:12 +1100<br>> >> From: Dallas.Warren@pharm.monash.edu.au<br>> >> Subject: RE: [gmx-users] large number of molecules<br>> >> To: gmx-users@gromacs.org<br>> >><br>> >> You are going to have to provide a lot more details than that if you want<br>> >> some help.<br>> >><br>> >><br>> >> What is “wrong results”? What is your input (copy and paste some commands<br>> >> in)? What is the output (copy and paste)? What makes you think the results<br>> >> are “wrong”? In what situations are they “right”? … and there are a lot<br>> >> more questions that could be asked ……<br>> >><br>> >><br>> >> Catch ya,<br>> >><br>> >> Dr. Dallas Warren<br>> >> Drug Delivery, Disposition and Dynamics<br>> >> Monash Institute of Pharmaceutical Sciences, Monash University<br>> >> 381 Royal Parade, Parkville VIC 3010<br>> >> dallas.warren@pharm.monash.edu.au<br>> >> +61 3 9903 9167<br>> >> ---------------------------------<br>> >> When the only tool you own is a hammer, every problem begins to resemble a<br>> >> nail.<br>> >><br>> >><br>> >> *From:* gmx-users-bounces@gromacs.org<br>> >> [mailto:gmx-users-bounces@gromacs.org] *On Behalf Of *ksm tprk<br>> >> *Sent:* Tuesday, 9 March 2010 8:33 AM<br>> >> *To:* gromacs users<br>> >> *Subject:* [gmx-users] large number of molecules<br>> >><br>> >><br>> >> Hello,<br>> >><br>> >><br>> >> I simulate carbon nanotube and basically I follow up<br>> >> http://cs86.com/CNSE/SWNT.htm<br>> >><br>> >> But when I increase the number of molecules (like 15000) , it gives me<br>> >> wrong results.<br>> >><br>> >> Do you know why this is happen?<br>> >><br>> >><br>> >> Thank you,<br>> >><br>> >> Kasim<br>> >><br>> >><br>> >> ------------------------------------------------------------------------<br>> >><br>> >> Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up<br>> >> now. <http://clk.atdmt.com/GBL/go/201469229/direct/01/><br>> >><br>> >><br>> >> ------------------------------------------------------------------------<br>> >> Hotmail: Powerful Free email with security by Microsoft. Get it now.<br>> >> <http://clk.atdmt.com/GBL/go/201469230/direct/01/><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>> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> ><br>> > ========================================<br>> > --<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://lists.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 www interface<br>> > 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>> Oliver Stueker<br>> Post-doctoral Fellow, Bader Lab<br>> Donnelly CCBR, University of Toronto, Canada<br>> http://baderlab.org<br>> phone: +1 (416) 978-0571<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.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></div> <br /><hr />Hotmail: Trusted email with Microsoft’s powerful SPAM protection. <a href='http://clk.atdmt.com/GBL/go/201469226/direct/01/' target='_new'>Sign up now.</a></body>
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