[gmx-users] Constraining a part of the system

[Justin Lemkul]

On 9/17/13 10:00 AM, HANNIBAL LECTER wrote:
> Is there a way to constraint bonds of a part of the system while keeping
> the other part flexible? For example for a simulation with two proteins, I
> would like to constraint the bonds of one and would like to keep the other
> flexible.
>
> I would prefer to use LINCS to constraint the system
>

Set the constraints explicitly in the topology of one protein using a 
[constraints] directive.  Then set "constraints = none" in the .mdp file.  The 
constraints read from the topology will override the .mdp setting while leaving 
all other bonds unconstrained.

-Justin

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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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