[gmx-users] Constraining a part of the system

[HANNIBAL LECTER]

Does anyone have proper parameters for CNTs ? I have been trying to perform
Simulations with finite CNTs. However, none of the parameters so far
(obtained from literature) seem to give the output temperatures equal to
set temperatures.

I have been looked into my input files time and again, but I could not
locate any bug so far. The problem is if I simulate my CNT with bonds
angles dihedrals and 1-4 interactions and constraint the bonds, the
temperature of the CNT seems to deviate far from the set temperature with
reasonable values of tau-t using the sd integrator in GROMACS.

Does anyone have parameters for CNTs such that they work with the SD
integrator with reasonable tau-t values?


On Tue, Sep 17, 2013 at 5:14 PM, HANNIBAL LECTER <hanniballecter13 at gmail.com
> wrote:

> @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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