[gmx-users] Make a rigid Nanoparticle

Justin Lemkul jalemkul at vt.edu
Thu May 31 16:35:22 CEST 2018

On 5/31/18 10:33 AM, Samieegohar, Mohammadreza wrote:
> Hi
> I am trying to make a completely rigid Au nanoparticle with harmonic potential bond and angle
> I am using a very big harmonic constant and still there is a small vibration in nanoparticle atoms
> Do you have an idea about how can I fixe the atom totally as rigid body?
> I do not want to use freeze them because my nanoparticle should move as a rigid body .

Many people have asked this same question in recent days; the answer is 
that GROMACS is not equipped to do rigid-body dynamics.

> Also I have another question :
> How can I make van der waals interaction zero between the nanoparticle atoms in coarse grained martini?

Define the interactions between all relevant atom types as zero in 



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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