[gmx-users] simulation with position constraint by a harmonic potential
liu4gre at gmail.com
Tue Sep 27 16:16:19 CEST 2011
It is weird why I always receive the digest of the mailing list but the
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
>> "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
> Liang Liu
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