Quoting pragya chohan <[EMAIL PROTECTED]>: > > > I wrote yes to generate velocity. Can that be a reason for the problem? Since > I am doing membrane simulation it is advised to do production runs in npt > thats the only other difference.
I think what Mark was asking for was a bit more detail on how you put your system together. It would be helpful to know (step by step) what you did, as that may highlight a problem. Also, what do you define as "deformed very much?" Some fluctuations are to be expected, and 250 ps is a relatively short time frame. In some of my bilayer simulations, the lipids look quite strange under NVT, but after a nanosecond or two or NPT they even out and behave normally. -Justin > ---------------------------------------- > > Date: Sat, 15 Dec 2007 06:03:27 +1100 > > From: [EMAIL PROTECTED] > > To: [email protected] > > Subject: Re: [gmx-users] problem with npt > > > > pragya chohan wrote: > > > > > > thanks for your help. > > > My system ran fine for 250 ps but later the bilayer deformed very much. > > > > What was your system preparation protocol - i.e. minimization and > > equilibration? See > > http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation > > > > Mark > > _______________________________________________ > > gmx-users mailing list [email protected] > > http://www.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 [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > _________________________________________________________________ > Post free property ads on Yello Classifieds now! www.yello.in > http://ss1.richmedia.in/recurl.asp?pid=220_______________________________________________ > gmx-users mailing list [email protected] > http://www.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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list [email protected] http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
