[gmx-users] Constraining a part of the system

[Justin Lemkul]

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.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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-- 
==================================================

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

==================================================