[gmx-users] Constraining a part of the system

[Dr. Vitaly Chaban]

the smart way is to constrain everything at once in MDP...
Dr. Vitaly V. Chaban


On Tue, Sep 17, 2013 at 10:50 PM, HANNIBAL LECTER
<hanniballecter13 at gmail.com> wrote:
> Is there a smart way of writing the constraint sections in the topology
> file other than entering the values manually ?
>
>
> On Tue, Sep 17, 2013 at 10:10 AM, rahul seth
> <rahul.seth.gromacs at gmail.com>wrote:
>
>> Thanks
>>
>>
>> On Tue, Sep 17, 2013 at 10:03 AM, Justin Lemkul <jalemkul at 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
>> >
>> > --
>> > ==============================**====================
>> >
>> > 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 <jalemkul at outerbanks.umaryland.edu>
>> | (410)
>> > 706-7441
>> >
>> > ==============================**====================
>> >
>> > --
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