Mark,
thanks for explanation again. 28 марта 2012 г. 16:04 пользователь Mark Abraham <[email protected]>написал: That can mean big restraint forces and tiny integration steps and lots of > tweaking and praying. > Yes I think this aproach could be usefull in my case. Actually I want to move some parts of the helices of my protein in the deired direction up to 6-10 A. There is the data showing that this new conformation is very unstabile and short-lived in the absense of some additional external factors. But also I've seen that application of big restrained forces perturbed the overal structure of my protein considerably. So the good sollution might be application of such forces with the position restraines simultaneously. What do you think about the most trivial aproach: e.g if I could not applied posres on the desired atoms and use default posres generated by pdb2gmx on the all atoms. At the same time I'm using more strongest distance restrains on the desired positions to move this atoms even the precense of weaker posres applied on this. Finally because posres act on the others atoms I can prevent destabilisation of the whole protein. Might this aproach be usefull? And what difference between forses of the posres ( 1000 kj) and disres must be to generate expected effect ? James > >
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