[gmx-users] Verify if position restrain was applied

[Justin Lemkul]

On 10/26/15 4:44 PM, Ebert Maximilian wrote:
> Thank you for your clarification that makes sense now in my simulation. Never the less is there an output per atom somewhere?
>

Everything is in the .tpr file.  Use gmx dump and redirect to a file and look 
through.

-Justin

> Thank you very much
>
>> On Oct 26, 2015, at 4:37 PM, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>>
>> On 26/10/15 21:06, Ebert Maximilian wrote:
>>> I saw that you can use gmx energy to select Position-Rest. and Constr.-rmsd but I was looking for the atom id on which the position restrains acted. Looking at my trajectory I am not sure if I did the correct configuration since my energy from gmx energy -> Position-Rest shows a maximum of 20kJ/mol but my molecule moved around its position with a restrain of 1000 1000 1000.
>>>
>>> Max
>>>
>>>> On Oct 26, 2015, at 4:02 PM, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>>>>
>>>> On 26/10/15 20:58, Ebert Maximilian wrote:
>>>>> Dear list,
>>>>>
>>>>> I wanted to know if there is a way to verify if the position restrain was applied correctly to the atoms in question. Couldn’t find anything in the log file.
>>>>>
>> restraint mean 1000 kJ/mol/nm^2, so 20 kJ/mol means 0.02 nm^2, or 0.14 nm for 1 atom.
>>>> How about position restraint energy?
>>>>
>>>>> Thank you,
>>>>>
>>>>> <ax
>>>>>
>>>>
>>>>
>>>> --
>>>> David van der Spoel, Ph.D., Professor of Biology
>>>> Dept. of Cell & Molec. Biol., Uppsala University.
>>>> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
>>>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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>>
>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
>> --
>> Gromacs Users mailing list
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>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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