Rahul,
I cannot answer your question, but have another one: you are combining
ntr=1/restraintmask-based restraints with nmropt=1-based restraints. I
vaguely remember that pmemd does not support this combination, i.e. that
it only supports one of these at the same time. Is that still the case,
do you run the simulation with sander?
Cheers,
Jan-Philip
On 22.04.2013 21:11, Rahul Banerjee wrote:
> Dear Amber users,,
>
> I am running equilibration simulation in presence of a finite positional restraint on all heavy atoms of my system. How can I reduce the restraint force gradually in 1000 steps? My reference structure is the starting structure of the simulation. I am using following script below. At the final step the restraint energy should be zero as the 'k' goes to zero. But it is not so. Am I wrong conceptually?
>
> With best regards,
> Rahul
>
> Equil
> &cntrl
> imin=0,irest=0,ntx=1,
> nstlim=1000,dt=0.002,
> ntc=2,ntf=2,
> cut=10.0, ntb=2, ntp=1, taup=2.0,
> ntwe=5, ntpr=5, ntwx=5, ntwr=5,
> ntt=3, gamma_ln=2.0, ig=-1
> temp0=300.0, nmropt=1,
> ntr=1, restraintmask=':1-120&!.H=', restraint_wt=8.0,
> /
> &wt
> TYPE='REST', istep1 =0, istep2 = 1000,
> value1 = 8.0, value2 = 0,
> /
> &wt type = 'END'
> /
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Received on Mon Apr 22 2013 - 14:30:03 PDT
