[gmx-users] Verify if position restrain was applied
David van der Spoel
spoel at xray.bmc.uu.se
Mon Oct 26 21:37:29 CET 2015
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.
>> 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,
>> 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
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