Hi Jan-Philip,
This combination works with Sander but not with PMEMD.
I do not understand though, why this option is not available. When NMR restraints can be reduced gradually, why not positional restraints?
With best regards,
Rahull
________________________________________
From: Jan-Philip Gehrcke [jgehrcke.googlemail.com]
Sent: Monday, April 22, 2013 5:11 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Reducing positional restraint gradually
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 Tue Apr 23 2013 - 07:00:03 PDT
