Thanks for your reply. In fact, I plan to study ion conduction through the peptide inserted in lipid membrane and acting as an ion channel. According to the literature, an ion across the membrane in less than 20 ns. Can I decide upon this information to apply pull code?
You simulated the protofibril structures for 100 ns, in another article 25 ns. Ok, if there is not any universal recipe for it, what do you suggest me? Try and error? Sincerely, Shima ----- Original Message ----- From: Justin Lemkul <jalem...@vt.edu> To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Friday, May 17, 2013 4:02 PM Subject: Re: [gmx-users] Re: Running Pull Code On 5/17/13 7:16 AM, Shima Arasteh wrote: > Thanks for your reply. > It' s around 5 nano seconds that I ran equilibration time on the system, and > the average pressure I see as a result, seems sensible. However I am not sure > if this criteria is sufficient? Others suggest to evaluate the box-dimension > changes using g_energy code to judge of sufficient equilibration time. > The box vectors won't tell you anything more than the pressure will since they're related quantities. The better question is, "What is a suitable starting structure for the system of interest?" The umbrella sampling tutorial (which everyone seems to take at literal face value as the only way to do things, which it is decidedly not) presents a simple, easy-to-understand method. In the paper I did (upon which I based the tutorial), I simulated the protofibril structures for 100 ns before I was confident they were suitably stable and representative of viable structures for doing SMD and US. Your mileage will vary and depends on the quality of the starting structure and what it is that you hope to determine. There is no magic recipe that is universal. -Justin > I appreciate your suggestion. > > > Sincerely, > Shima > > > ----- Original Message ----- > From: Thomas Schlesier <schl...@uni-mainz.de> > To: gmx-users@gromacs.org > Cc: > Sent: Friday, May 17, 2013 3:30 PM > Subject: [gmx-users] Re: Running Pull Code > > The three steps (EM, NVT and NPT) are to equilibrate the system. How > much time these steps need depends on the system. But i would assume a > ouple of nanosecounds are sufficient for most systems. You could look > into the literature, how long other people equilibrate systems which are > similar to ours. > If the system is equilibrated, you an start to perform the pulling > simulation to obtain the individual structure for the later umbrella > sampling. > > Greetings > Thomas > > Am 17.05.2013 07:46, schrieb gmx-users-requ...@gromacs.org: >> Hi, >> >> I have a system composed of POPC/peptide/water/ions. I aim to study ion >> conduction through the peptide using umbrella sampling. >> I built the system and ran EM, NVT, NPT successfully, but have not run md >> yet. I' d like to know if the system is required of passing a few >> nanoseconds md? Or I might be able to go to Umbrella Sampling straight after >> NPT? >> As I studied in Justin's tutorial, running pull code is done after some >> typical steps of every simulation ( EM, NVT, NPT). But I dont know if is >> correct generally for other systems as well? >> >> Would you please give me any suggestions? >> >> >> Thanks in advance. >> Sincerely, >> Shima? > -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist 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-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
