[gmx-users] make a rigid nanoparticle (internally freeze body while it can move as a rigid body )
mohammadreza.samiee at Howard.edu
Thu May 31 16:36:58 CEST 2018
Thank you Abraham .
Already I used the harmonic bond with a big harmonic constant but I have a small vibration yet
do you know how can I remove van der waals interaction totally between the atoms of Nanoparticle ?
may be it the small vibration is because of van der waals.
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Mark Abraham <mark.j.abraham at gmail.com>
Sent: Tuesday, May 22, 2018 11:23:35 AM
To: gmx-users at gromacs.org
Cc: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] make a rigid nanoparticle (internally freeze body while it can move as a rigid body )
This cannot be done with GROMACS, there is no general support for rigid
On Tue, May 22, 2018 at 5:15 PM Samieegohar, Mohammadreza <
mohammadreza.samiee at howard.edu> wrote:
> I need to make a rigid Gold nanoparticle to run a coarse grained
> simulation. my gold nanoparticle will penetrate in a lipid membrane
> I have built the initial structure by Material studio. This nanoparticle
> must be a internally freeze body while it can move as a rigid body
> My question is , how can I make a rigid particle in Gromacs ? the particle
> should move as whole body in all directions while all of the atoms are fix
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