[gmx-users] Re: Simulation in the high temperature conditions

[James Starlight]

Justin,


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)

I've tried

genrestr -f start.gro -n index.ndx -disre -disre_dist 0.7 -disre_frac 0.7
-disre_up2 1.0

>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
0.069-0.395 etc.

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 ?


James

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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