[gmx-users] Verify if position restrain was applied

[Ebert Maximilian]

Thank you for your clarification that makes sense now in my simulation. Never the less is there an output per atom somewhere?

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.
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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
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