[gmx-users] position restraint single atom

[Andrea Spitaleri]

Hi there,

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.

Thanks

and


-- 
Andrea Spitaleri PhD
Computational mOdelling of NanosCalE and bioPhysical sysTems - CONCEPT Lab
ISTITUTO ITALIANO DI TECNOLOGIA
Via Morego 30, 16163 - Genova, Italy
https://iit.it/research/lines/computational-modelling-of-nanoscale-and-biophysical-systems
cell: +39 3485188790
https://iit.it/andrea-spitaleri
ORCID: http://orcid.org/0000-0003-3012-3557