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ya i removed every water molecule that entered the bilayers. after pr should i do nvt before doing npt? i am doing position restrain also under npt.<BR><BR>> Date: Mon, 17 Dec 2007 11:27:01 +0200<BR>> From: neamtuandrei@gmail.com<BR>> To: gmx-users@gromacs.org<BR>> Subject: Re: [gmx-users] problem with npt<BR>> <BR>> Hi,<BR>> have you checked if there is no water inside the membrane after the<BR>> use of genbox?<BR>> <BR>> On Dec 16, 2007 1:35 PM, Mark Abraham <Mark.Abraham@anu.edu.au> wrote:<BR>> > pragya chohan wrote:<BR>> > ><BR>> > > i started with the lipid coordinates from peter tieleman and removed the<BR>> > > water. then i added water by genbox.<BR>> > > I did energy minimization followed by position restrain, which I removed<BR>> > > gradually. all of it was done under npt. I carried out npt for 250<BR>> > > ps. During the next 250 ps npt run the bilayers separated and deformed.<BR>> ><BR>> > Usually NVT to get the temperature right before relaxing to NPT to let<BR>> > the density equilibrate can be good idea. Look at how much your box<BR>> > changed size during your NPT to see if this effect is causing problems.<BR>> ><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>> 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 /><hr />Fly HYD-BLR for Rs.499 Log on to MakeMyTrip! <a href='http://ss1.richmedia.in/recurl.asp?pid=266' target='_new'>Check it out!</a></body>
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