AMBER Archive (2007)

Subject: Re: AMBER: TIP5P questions

From: David A. Case (case_at_scripps.edu)
Date: Thu Sep 13 2007 - 19:17:12 CDT

On Tue, Sep 11, 2007, Prashanth Athri wrote:

> I am having the following question regarding TIP5P usage. I am comparing results of TIP5P and TIP3P water (trying) wrt DNA+ ligand simulation.
>
> When I use the following commands:
> 1. solvateoct co TIP3PBOX 8.0
> 2. solvateoct co TP5 8.0

Some one (e.g. me) should make a TIP5PBOX file and add it to the distribution.

Solvating with a pre-equilibrated box gives a better starting point than just
solvating with a single molecule, although both should work: the latter will
just need more equilibration. With item 2, you may have to play with the
radius (8.0 in your example) to get the number of waters (or final box size)
you want. Since the starting density is low, your final box will be quite a
bit smaller than the initial one, so you need to adjust for that by asking for
a larger box to begin with.

...good luck....dac 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  skype:                 dacase
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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