[gmx-users] Re: How to differenciate Decane and Dodecane with the Martini force field

[ABEL Stephane 175950]

Thank you Tsjerk for your quick response. 

A bientot 

Stephane

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Message: 2
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>
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        <CABzE1Si6U3E=Z8Yp_ynft4aBReQznVHNWeRXF20-zU-m60p1fA at mail.gmail.com>
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Hi Stephane,

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
kinetic.

Cheers,

Tsjerk


--
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada