[gmx-users] Verify if position restrain was applied

[David van der Spoel]

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