Hi Karim, On Mon, Mar 8, 2010 at 18:11, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > ksm tprk wrote: >> >> My mdp file is what http://cs86.com/CNSE/SWNT.htm has. I used nose-hoover >> for Tcouple. >> and the beginning of mdp code looks like: >> > > Partial information is useless. Post the whole .mdp file; there are plenty > of parameters that can be set incorrectly or inconsistently.
In addition to Justin, you haven't told us even which forcefield you are using. I hope it's not ffgmx as it is in the reference you gave us. Search the Archive and the Gromacs wiki for reasons not to use ffgmx. Oliver > -Justin > >> ; RUN CONTROL PARAMETERS >> integrator = md >> ; Start time and timestep in ps >> tinit = 0 >> dt = 0.0005 >> nsteps = 10000000 >> ; For exact run continuation or redoing part of a run >> init_step = 0 >> ; mode for center of mass motion removal >> comm-mode = Angular >> ; number of steps for center of mass motion removal >> nstcomm = 1 >> ; group(s) for center of mass motion removal >> comm-grps = >> >> >> I used gromacs 3.3.3 and in the vacuum. I applied the heat first around 10 >> layers. >> after I finished my simulation and look at the edr file, the result >> temperatures are higher than what I gave. It looks like it generates heat by >> it self. >> But when I do same simulation with less molecules such as 6000, it looks >> fine. >> >> >> >> >> ------------------------------------------------------------------------ >> Date: Tue, 9 Mar 2010 08:57:12 +1100 >> From: dallas.war...@pharm.monash.edu.au >> Subject: RE: [gmx-users] large number of molecules >> To: gmx-users@gromacs.org >> >> You are going to have to provide a lot more details than that if you want >> some help. >> >> >> What is “wrong results”? What is your input (copy and paste some commands >> in)? What is the output (copy and paste)? What makes you think the results >> are “wrong”? In what situations are they “right”? … and there are a lot >> more questions that could be asked …… >> >> >> Catch ya, >> >> Dr. Dallas Warren >> Drug Delivery, Disposition and Dynamics >> Monash Institute of Pharmaceutical Sciences, Monash University >> 381 Royal Parade, Parkville VIC 3010 >> dallas.war...@pharm.monash.edu.au >> +61 3 9903 9167 >> --------------------------------- >> When the only tool you own is a hammer, every problem begins to resemble a >> nail. >> >> >> *From:* gmx-users-boun...@gromacs.org >> [mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *ksm tprk >> *Sent:* Tuesday, 9 March 2010 8:33 AM >> *To:* gromacs users >> *Subject:* [gmx-users] large number of molecules >> >> >> Hello, >> >> >> I simulate carbon nanotube and basically I follow up >> http://cs86.com/CNSE/SWNT.htm >> >> But when I increase the number of molecules (like 15000) , it gives me >> wrong results. >> >> Do you know why this is happen? >> >> >> Thank you, >> >> Kasim >> >> >> ------------------------------------------------------------------------ >> >> Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up >> now. <http://clk.atdmt.com/GBL/go/201469229/direct/01/> >> >> >> ------------------------------------------------------------------------ >> Hotmail: Powerful Free email with security by Microsoft. Get it now. >> <http://clk.atdmt.com/GBL/go/201469230/direct/01/> >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Oliver Stueker Post-doctoral Fellow, Bader Lab Donnelly CCBR, University of Toronto, Canada http://baderlab.org phone: +1 (416) 978-0571 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php