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

[James Starlight]

Justin,


10 апреля 2012 г. 16:21 пользователь Justin A. Lemkul <jalemkul at vt.edu>написал:

>
> I have never used the bd integrator so I cannot offer any help here.  I
> don't see any magical reason why you should expect it to enhance sampling
> though.


 I've found in the literature that this integrator could rise the
integration-time-step from common 1-2fs used with the MD-integrator.



By the way I've tried to test my system equilibrated in the hight
temperature in different conditions. As the consequence when I've removed
all posres ( on the last stage of equilibration it's value was 200 for
backbone atoms only) from my protein the alpha helixes have been
destabilised already after 3ns of such unconstrained simulation ( ref_t=
700k).

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. It's known that conformation
transitions wich I want to ssample accompanied by the large scale motions
in the helical segments ( up to 10-15 A). At the same time such big
fluctuations on the other atoms may destabiise regions wich are more rigid.
Should I define several sets of restrains for my protein to allow one
regions move with bigger amplitudes in comparison with rigid fragments ?

3- Finally alternative aproach is the ussage of common temperature (
ref_t=310k) in the production run but using starting velocities obtained
from the nvt equilibrration obtained with the hight ( 700k) temperature.
Can I enhance sampling using that starting conditions ?


What from this three strategies is the most suitable? IS there any
alternative ways for such high-temperature simulation ?


Thanks for help again,


James
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