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. I
came up with this DISANG file:
# time-dependent distance restraint
&rst
iat=5085, 5259,
ifvari=1,
r1=50.5, r2=50.5, r3=50.5, r4=50.5,
r1a=20.5, r2a=20.5, r3a=20.5, r4a=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
pmemd is not exiting while parsing this DISANG file. Is this expected to
produce the same time-dependent distance restraint as the top-most
configuration in this mail?
It looks like the required restraint functionality is available in
pmemd. However, with jar=1 the user is more or less arbitrarily
restricted in his freedom to set up further restraints. Does this
restriction make sense? Would it be a rather complex task to make pmemd
with jar=1 support further restraints? Is there anything I can do to help?
Thanks,
Jan-Philip
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Received on Thu Apr 25 2013 - 05:30:02 PDT
