[gmx-users] Make a rigid Nanoparticle

[Justin Lemkul]

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 
[nonbond_params].

-Justin

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

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