[gmx-users] Re: How to differenciate Decane and Dodecane with the Martini force field
ABEL Stephane 175950
Stephane.ABEL at cea.fr
Tue Feb 26 19:01:25 CET 2013
Thank you Tsjerk for your quick response.
Date: Tue, 26 Feb 2013 16:53:51 +0100
From: Tsjerk Wassenaar <tsjerkw at gmail.com>
Subject: Re: [gmx-users] How to differenciate Decane and Dodecane with
the Martini force field
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
<CABzE1Si6U3E=Z8Yp_ynft4aBReQznVHNWeRXF20-zU-m60p1fA at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
It's one of the caveats of a reduced resolution model. You loose
detail, like the distinction between decane and dodecane. Although,
there are two bonds and an angle to make a difference.
> Additionally, can i change of the mass of each bead the mass of Decane/3 in the itp file instead of the default mass for C1 (72 AMU) ?
You can do anything you like in modeling. It may make sense :) But
different masses on the beads won't give you differences other than
Tsjerk A. Wassenaar, Ph.D.
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
More information about the gromacs.org_gmx-users