[gmx-users] position restraint single atom
andrea.spitaleri at iit.it
Wed Feb 15 15:37:25 CET 2017
I have a dsDNA and I'd like to restraint just two atoms, O3' and O5'
respectively, in order to mimic the anchor-like to a solid support. I
have create ad hoc posre.itp file but for some reason the DNA-anchor is
moving too much from the starting position. I would expect more rigidity
around the two atoms. Does it sound strange to you? I mean, I was
expecting oscillation of the whole DNA but keeping the anchors fixed.
Are two atoms too little to get this kind behaviour (i.e. DNA-anchor)?
The constant force is 1000 kJ/mol nm^2.
Any help/comments on this are welcome.
Andrea Spitaleri PhD
Computational mOdelling of NanosCalE and bioPhysical sysTems - CONCEPT Lab
ISTITUTO ITALIANO DI TECNOLOGIA
Via Morego 30, 16163 - Genova, Italy
cell: +39 3485188790
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