<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
<HTML>
<HEAD>
<META NAME="Generator" CONTENT="MS Exchange Server version 6.5.6944.0">
<TITLE>Re: [gmx-users] Water density</TITLE>
</HEAD>
<BODY>
<DIV id=idOWAReplyText97733 dir=ltr>
<DIV dir=ltr><FONT face=Arial color=#000000 size=2>Thanks david for reply. I
have been trying to fix density of a water box at 300k temp. At first
I scaled the density of spc216.gro using editconf and then I
have created spc water box using genbox and scaled the water box using
editconf -density 1000. Finally I allowed
some vacuum in z direction using editconf again and run
for a short time( 2ns) under no pressure and checked using g_density
which giving me less density than what I start off. Is it because of
vaccum? </FONT></DIV>
<DIV dir=ltr> </DIV>
<DIV dir=ltr><FONT face=Arial color=#000000 size=2>regards,</FONT></DIV></DIV>
<DIV id=idSignature77081 dir=ltr>
<DIV RE>Abu Naser
<DIV RE><PRE></PRE>
<DIV RE>School Of Life Sciences </DIV>
<DIV RE>Heriot-Watt University </DIV>
<DIV RE>Edinburgh EH14 4AS </DIV>
<DIV RE>Email: <A href="mailto:mn2@hw.ac.uk">mn2@hw.ac.uk</A></DIV>
<DIV RE>Phone: +44(0)1314518265 </DIV>
<DIV RE>Fax : +44(0) 131 451 3009 </DIV>
<DIV RE>
<DIV RE>
<DIV RE>
<DIV RE>
<DIV RE>
<DIV RE><PRE></PRE>
<DIV RE>
<DIV RE>
<DIV RE><PRE></PRE></DIV>
<DIV RE>
<DIV RE>
<DIV RE><PRE></PRE></DIV></DIV></DIV></DIV></DIV></DIV></DIV></DIV></DIV></DIV></DIV></DIV></DIV></DIV>
<DIV dir=ltr><BR>
<HR tabIndex=-1>
<FONT face=Tahoma size=2><B>From:</B> gmx-users-bounces@gromacs.org on behalf of
David van der Spoel<BR><B>Sent:</B> Mon 20/02/2006 2:02 PM<BR><B>To:</B>
Discussion list for GROMACS users<BR><B>Subject:</B> Re: [gmx-users] Water
density<BR></FONT><BR></DIV>
<DIV>
<P><FONT size=2>Naser, Md Abu wrote:<BR>> Hi All,<BR>><BR>> When I run
a water box after fixing its density(1kg/L) using editconf,<BR>> the density
of the box always is going down to 955gm/L. I have been<BR>> wondering why
this is happening. Can anyone give some clue?<BR>><BR>details
please.<BR><BR>> Abu Naser<BR>><BR>> School Of Life Sciences<BR>>
Heriot-Watt University<BR>> Edinburgh EH14 4AS<BR>> Email:
mn2@hw.ac.uk<BR>> Phone: +44(0)1314518265<BR>> Fax : +44(0) 131 451
3009<BR>><BR>><BR>><BR>><BR>> Abu Naser<BR>><BR>> School Of
Life Sciences<BR>> Heriot-Watt University<BR>> Edinburgh EH14 4AS<BR>>
Email: mn2@hw.ac.uk<BR>> Phone: +44(0)1314518265<BR>> Fax : +44(0) 131 451
3009<BR>><BR>><BR>><BR>><BR>><BR>>
------------------------------------------------------------------------<BR>><BR>>
_______________________________________________<BR>> gmx-users mailing
list gmx-users@gromacs.org<BR>> <A
href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A><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
<A
href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</A><BR><BR><BR>--<BR>David.<BR>________________________________________________________________________<BR>David
van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<BR>Dept. of Cell
and Molecular Biology, Uppsala University.<BR>Husargatan 3, Box 596,
75124 Uppsala, Sweden<BR>phone:
46 18 471 4205 fax: 46 18 511
755<BR>spoel@xray.bmc.uu.se spoel@gromacs.org <A
href="http://folding.bmc.uu.se">http://folding.bmc.uu.se</A><BR>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<BR>_______________________________________________<BR>gmx-users
mailing list gmx-users@gromacs.org<BR><A
href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A><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 <A
href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</A><BR></FONT></P></DIV>
</BODY>
</HTML>