[gmx-users] Verify if position restrain was applied

[Ebert Maximilian]

Thanks I didn’t know the dump command.

Good evening

On Oct 26, 2015, at 4:50 PM, Justin Lemkul <jalemkul at vt.edu<mailto:jalemkul at vt.edu>> wrote:



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<mailto: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<mailto: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



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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<mailto:spoel at xray.bmc.uu.se>    http://folding.bmc.uu.se
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
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University of Maryland, Baltimore
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jalemkul at outerbanks.umaryland.edu<mailto:jalemkul at outerbanks.umaryland.edu> | (410) 706-7441
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