[gmx-users] How to put constraint

[Justin Lemkul]

On 5/21/18 4:27 PM, Tom wrote:
> Dear GMX experts:
>
>
> I want to constraint atoms inside a polymer.
>
> The atoms are fixed to their relative positions,
>
> but the whole polymer can move as a rigid body.
>
>
> Can we use LINCS?

GROMACS is not well suited to rigid-body dynamics, and formally it's not 
even supported. One could assign a series of constraints, but that's 
generally unstable. I'd suggest looking into different simulation 
packages that natively support rigid-body dynamics.

-Justin

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

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