[gmx-users] simulation with position constraint by a harmonic potential

[Liu, Liang]

It is weird why I always receive the digest of the mailing list but the
specific topic?

On Tue, Sep 27, 2011 at 9:14 AM, Liu, Liang <liu4gre at gmail.com> wrote:

> > Thanks.
>> >
>> > Is this position restraint same to the one "Position Restrained MD". I
>> > see some tutorial shows there are always three step to perform a
>> > simulation: Energy minimization, Position Restrained MD and MD
>> Simulation.
>>
>> "Always" is too strong, but this is common.
>>
>>
>> > Is it possible to fulfill the position restraint during Position
>> > Restrained MD? Thanks.
>>
>> Yes, hence the name. How well they can be fulfilled depends on the
>> initial and simulation conditions.
>>
>
> Thanks for this information.
> But how to perform a harmonic potential to all the heavy atoms of RNA?
> Justin said this one should be adjusted in the posre.itp file, and what I
> see in the file is all 1000. Does this means k=1000 in the equation of E = k
> (r-r0)^2?
> Thanks.
>
>
>>
>> Mark
>>
>
> --
> Best,
> Liang Liu
>



-- 
Best,
Liang Liu
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