[gmx-users] Re: Simulation in the high temperature conditions
jmsstarlight at gmail.com
Wed Apr 11 09:20:53 CEST 2012
I have not quite sure about methodology of aplication of such harmonic
distance restrains yet.
E.g I want to constraint distancec of the backbone atoms of my protein
within 7 A ( to allow deviation of all backnones up to 7 A)
genrestr -f start.gro -n index.ndx -disre -disre_dist 0.7 -disre_frac 0.7
>From this I've obtained for first 5 backbone atoms below disres
1 5 1 0 1 0.0441928 0.250426 1.25043 1
1 10 1 1 1 0.0697795 0.395417 1.39542 1
1 12 1 2 1 0.101657 0.576059 1.57606 1
1 14 1 3 1 0.138237 0.783341 1.78334 1
1 15 1 4 1 0.160509 0.909554 1.90955 1
so the atoms 1 and 5 would be unconstrained if the distance between them
would be 0.004-0.25, atoms 1 and 10 would be constrained within distance
I'm not quite understood from manual if the disre_dist exactly that range
value ralative atom coordinate in the start.gro ? What is the -desre_frac
and in what cases in could be usefull ?
10 апреля 2012 г. 18:25 пользователь Justin A. Lemkul <jalemkul at vt.edu>написал:
> So I suppose that the presence of the some constrained factor is needed
>> to prevent destabilisation but allow conformation sampling. I see three
>> alternative ways of my production MD run with enhanced sampling.
>> 1- First of all as the most trivial way I'm thinking of using soft posres
>> applied on backbone atoms only with the constained value ( 50-100 kj*nm2)
>> corresponded to the energy of the thermal motion.
>> 2- Also I've thought about application of the harmonic
>> distance_restraince (instead of posres) on the all backbone atoms exept of
>> flexible loops where this disres must be in the longer range ( e.g up to
>> 15-20A) but I could not realise about usefullness of such aproach because I
>> cant define value for such disres for the atoms in helixes.
> Sure you can. Use genrestr with a suitable index group. The use of lots
> of distance restraints precludes the use of DD, so you're limited to using
> mdrun -pd, which is a lot slower and may counteract any perceived benefit
> in terms of simulation time.
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