Hello all,
I am running a simulation under AMBER16 using pmemd.cuda. I am attempting
to use NMR restraints to hold a ligand in place during equilibration, then
gradually release the restraints in preparation for production run.
To accomplish this, I am using 'nmropt=1' under the '&cntrl' list and
afterward:
&wt type='REST', istep1=1,istep2=200000,
value1=1.0,value2=0.0, !ramp down restraint to 0
&end
&wt type='DUMPFREQ', istep1=1000,
&end
&wt type='END',
&end
DISANG=step4.4_equilibration.rest
DUMPAVE=step4.4_equilibration.distout
The nmr restraint file (step4.4_equilibration.rest) reads:
&rst
ixpk= 0, nxpk= 0, iat=1276, 7908, r1=0.0, r2=2.0, r3=2.0, r4=4.0,
rk2=50.0, rk3=50.0, ir6=0, ialtd=0,
&end
Upon examination of the resulting trajectory, amber output and distout
files, I see that the distance between the two restrained atoms remains
roughly constant at about 2.8 to 3.0 Å
If, however, I set rk2=0.0 and rk3=0.0, the restrained atoms move away
rapidly from their starting postion at about 2.9 to a distance of about 4.5
over the 200ps trajectory.
Is this a bug or am I doing something wrong in my setup?
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Received on Fri Jul 22 2016 - 16:30:02 PDT
