On 04/25/2013 02:08 PM, Jan-Philip Gehrcke wrote:
> Hello,
>
> I am trying to run a jar=1 simulation while a few torsions of the system
> are required to be controlled via restraints. The corresponding DISANG
> file looks like that:
>
> # jar=1: time-dependent distance restraint (SMD)
> &rst
> iat=5085, 5259,
> r2=50.5,
> r2a=20.5,
> rk2=100,
> &end
>
> # torsional restraint
> &rst
> iat=5241, 5243, 5244, 5249,
> r1=-82, r2=-67, r3=-57, r4=-42, rk2=10, rk3=10,
> &end
>
> This works in sander. In pmemd, however, this is not supported. A
> beautiful error message in the mdout file appears :-)
>
> "In Jarzynsky runs, there must only one restrain, stopping program"
>
> For my simulations, it is crucial that I am able to run them with
> pmemd(.cuda).
>
> W.r.t to the Jarzynsky implementation, I am only interested in the
> time-dependent distance restraint. A solution would be if I can achieve
> the same restraint type with other settings being supported by pmemd.
It looks like this would be one working replacement of the SMD distance
restraint:
&rst
iat=5085, 5259,
ifvari=1,
nstep1=0,
nstep2=25000,
r1=45.5, r2=50.5, r3=50.5, r4=55.5,
r1a=15.5, r2a=20.5, r3a=20.5, r4a=25.5,
rk2=100,
rk2a=100,
rk3=100,
rk3a=100,
&end
It works in pmemd if combined with various other NMR restraints.
I am irritated by the fact that there are two different explanations of
the "ifvari" setting in the Amber12.pdb (page 203 and 204). The one
stating "Note that you *must* specify an explicit value for nstep1 and
nstep2 if you use this option" seems to be right. However, I would be
more happy about the nstep2 default being the end of the simulation.
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Received on Thu Apr 25 2013 - 08:00:04 PDT
