Dear Chaiann,
> I am trying to create a cyclohexane box for my simulation. I
> am using the
> input for under the folder "solvent" in the amber directory
> and also the
> input file from the web. I am getting density of less than
> 0.4 at 300K after
> 50ps MD, which is the initial density when i solvate my
> cyclohexane (chair
> conformation) with a box of cyclohexane. Can anyone help?
> Attached is the
> PDB file of the cyclohexane and prepin file. Thanks.
Are you running constant pressure (ntb=2, ntp=1)? The default for periodic
boundaries is to run constant volume (ntb=1). In this case the box size will
be fixed at the value setup by Leap (a not very good guess at the density)
and thus the density will not change.
With constant pressure you should be able to equilibrate to a density of
around 0.78 g/cm^3 or so for cyclohexane. Although you may need more than
50ps of equilibration to reach an equilibrate density.
If you still have problems please post your prmtop, inpcrd, mdout and mdin
files.
All the best
Ross
/\
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|\oss Walker
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk | PGP Key available on request |
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Received on Thu Nov 03 2005 - 05:53:00 PST
