On 9/17/13 4:50 PM, HANNIBAL LECTER wrote:
Is there a smart way of writing the constraint sections in the topology
file other than entering the values manually ?
Write a script that parses the [bonds] directive of the post-processed topology
(output by grompp -pp) and write the relevant fields to a [constraints] directive.
-Justin
On Tue, Sep 17, 2013 at 10:10 AM, rahul seth
<rahul.seth.grom...@gmail.com>wrote:
Thanks
On Tue, Sep 17, 2013 at 10:03 AM, Justin Lemkul <jalem...@vt.edu> wrote:
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.
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Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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