[gmx-users] Constraining a part of the system

[HANNIBAL LECTER]

Yes. That is the way to go about it. I was hoping for a more lazy
approach... Thanks anyways.


On Tue, Sep 17, 2013 at 5:07 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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 <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 <jalemkul at outerbanks.umaryland.edu> | (410)
> 706-7441
>
> ==============================**====================
>
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