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<BR>i started with the lipid coordinates from peter tieleman and removed the water. then i added water by genbox.<BR>
I did energy minimization followed by position restrain, which I removed gradually. all of it was done under npt. I carried out npt for 250 ps. During the next 250 ps npt run the bilayers separated and deformed. <BR>> Date: Sat, 15 Dec 2007 09:53:06 -0500<BR>> From: jalemkul@vt.edu<BR>> To: gmx-users@gromacs.org<BR>> Subject: RE: [gmx-users] problem with npt<BR>> <BR>> Quoting pragya chohan <pragyachohan@hotmail.com>:<BR>> <BR>> ><BR>> ><BR>> > I wrote yes to generate velocity. Can that be a reason for the problem? Since<BR>> > I am doing membrane simulation it is advised to do production runs in npt<BR>> > thats the only other difference.<BR>> <BR>> I think what Mark was asking for was a bit more detail on how you put your<BR>> system together. It would be helpful to know (step by step) what you did, as<BR>> that may highlight a problem. Also, what do you define as "deformed very<BR>> much?" Some fluctuations are to be expected, and 250 ps is a relatively short<BR>> time frame. In some of my bilayer simulations, the lipids look quite strange<BR>> under NVT, but after a nanosecond or two or NPT they even out and behave<BR>> normally.<BR>> <BR>> -Justin<BR>> <BR>> > ----------------------------------------<BR>> > > Date: Sat, 15 Dec 2007 06:03:27 +1100<BR>> > > From: Mark.Abraham@anu.edu.au<BR>> > > To: gmx-users@gromacs.org<BR>> > > Subject: Re: [gmx-users] problem with npt<BR>> > ><BR>> > > pragya chohan wrote:<BR>> > > ><BR>> > > > thanks for your help.<BR>> > > > My system ran fine for 250 ps but later the bilayer deformed very much.<BR>> > ><BR>> > > What was your system preparation protocol - i.e. minimization and<BR>> > > equilibration? See<BR>> > > http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation<BR>> > ><BR>> > > Mark<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>> > Post free property ads on Yello Classifieds now! www.yello.in<BR>> ><BR>> http://ss1.richmedia.in/recurl.asp?pid=220_______________________________________________<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>> <BR>> ========================================<BR>> <BR>> Justin A. Lemkul<BR>> Graduate Research Assistant<BR>> Department of Biochemistry<BR>> Virginia Tech<BR>> Blacksburg, VA<BR>> jalemkul@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://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 /><hr />Post free auto ads on Yello Classifieds now! <a href='http://ss1.richmedia.in/recurl.asp?pid=255' target='_new'>Try it now!</a></body>
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