AMBER Archive (2006)

Subject: Re: AMBER: PCA results with explicit Vs Implicit solvation

From: Angelo (angelo_at_holmes.cancres.nottingham.ac.uk)
Date: Mon Nov 06 2006 - 11:14:47 CST

Hi,

You could try the explicit solvent simulation and compare them. It's a
bit of more work but....you will have an answer in the end.

Angelo

Keerthi Gottipati wrote:

> Hi all,
>
> I would like to know how(if at all) a choice of solvation method (i.e.
> implicit vs explicit) would reflect on the final analysis of a peptide
> (115 residue) if I'm using PCA to extract any conspicuous domain
> motions. I've analysed the trajectory from a GB simulation(1ns) and
> wondering if the overall behaviour would be any different with
> explicit solvent conditions.
>
> Thanks in advance,
> Keerthi.
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu

This message has been checked for viruses but the contents of an attachment
may still contain software viruses, which could damage your computer system:
you are advised to perform your own checks. Email communications with the
University of Nottingham may be monitored as permitted by UK legislation.

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu