[gmx-users] Constraining a part of the system

[HANNIBAL LECTER]

@Vitaly. Yes you are right. However, I noticed that if I do not constraint
the bonds in my CNT my simulations run fine. It is indeed surprising to me
but I do not have much experience with simulating CNTs and if not
constraining the bonds seem to get things done, I think it is a viable
option. But still need to test a lot of things before I can decide on the
final settings.


On Tue, Sep 17, 2013 at 5:11 PM, HANNIBAL LECTER <hanniballecter13 at gmail.com
> wrote:

> 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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