Dear All,
I am refining the duplex DNA structure using NOESY volume restraints and
restrained molecular dynamics simulations. In some cases, at a high
restraining potential (35 kcal), changes in sugar chirality (C1', C2',
C3' or C4' atoms) were observed during the simulation (time scale 10-100
ns). This potential value was taken to increase the impact of NMR
restraints in total energy. Is this a high potential wall problem
(atom's movement algorithm under high potential/force) or something else?
Here input file for simulation:
&cntrl
imin=0, irest=1, ntx=5,
nstlim=200000, dt=0.002,
ntf=1, ntc=1, ntb=0,
ntpr=500, ntwx=500, ntwr=500,
cut=999.0,
igb=1, saltcon=0.1,
ntt=2, temp0=300.0,
nmropt=2, ipnlty=1, mxsub=10, tausw=0.101, pencut=-1,
/
&wt type='NOESY', istep1=0,istep2=200000,value1=35.0,
value2=35.0, /
&wt type='END' /
NOESY=vol.rst
LISTOUT=POUT
and beginig of vol.rst file:
&noeexp
omega = 600,
npeak=55,57,61, -1,
taurot=3,
taumet=0.04,
oscale=4.37e-5,
id2o=1,
emix = 0.1, 0.2, 0.4,
ihp(1,1) = 10, jhp(1,1) = 7, aexp(1,1) = 366.79999, arange(1,1) = 36.68,
...
Best regards,
Alexander Lomzov
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Received on Wed Nov 11 2020 - 22:00:02 PST
