Dear Ross:
Thanks for your reply. I did use constant pressure where (ntb=2, ntp=1).
I somehow found the right way to doing it but it is rather strange.
Initially I am using antechamber to create the prepin file from the PDB file
that I download from www.molecularmodels.ca
It is these prmtop and inpcrd files create from this prepin file are not
working as the density is decreasing from the very beginning.
Colleague fo mine suggest that delete the H from the prepin file and use
Xleap to build the H back into the structure and save as PDB file, then
create a new prepin file from this new PDB file. This is time the density is
increasing to 0.74 after 150ps of MD.
So I do not really know what is going wrong but it seems to work this way.
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From: <i>"Ross Walker"
<ross.rosswalker.co.uk></i><br>Reply-To:
<i>amber.scripps.edu</i><br>To:
<i><amber.scripps.edu></i><br>Subject: <i>RE: AMBER: Density of
Cyclohexane box</i><br>Date: <i>Wed, 2 Nov 2005 20:52:32 -0800</i><br>Dear
Chaiann,<br><br> > I am trying to create a cyclohexane box for my
simulation. I<br> > am using the<br> > input for under the folder
"solvent" in the amber directory<br> > and also the<br> >
input file from the web. I am getting density of less than<br> > 0.4 at
300K after<br> > 50ps MD, which is the initial density when i solvate
my<br> > cyclohexane (chair<br> > conformation) with a box of
cyclohexane. Can anyone help?<br> > Attached is the<br> > PDB file of
the cyclohexane and prepin file. Thanks.<br><br>Are you running constant
pressure (ntb=2, ntp=1)? The default for periodic<br>boundaries is to run
constant volume (ntb=1). In this case the box size will<br>be fixed at the
value setup by Leap (a not very good guess at the density)<br>and thus the
density will not change.<br><br>With constant pressure you should be able to
equilibrate to a density of<br>around 0.78 g/cm^3 or so for cyclohexane.
Although you may need more than<br>50ps of equilibration to reach an
equilibrate density.<br><br>If you still have problems please post your
prmtop, inpcrd, mdout and mdin<br>files.<br><br>All the
best<br>Ross<br><br>/\<br>\/<br>|\oss Walker<br><br>| Department of
Molecular Biology TPC15 |<br>| The Scripps Research Institute |<br>| Tel: +1
858 784 8889 | EMail:- ross.rosswalker.co.uk |<br>|
http://www.rosswalker.co.uk | PGP Key available on request |<br><br>Note:
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Received on Fri Nov 04 2005 - 03:53:00 PST
