Re: [AMBER] Minimization and equilibration with SANDER.MPI and production with PMEMD.cuda ??

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 12 Aug 2014 12:15:24 -0400

On Tue, Aug 12, 2014 at 10:45 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com>
wrote:

> Again,
> as you mentioned I can use position restrain with PMEMD.cuda. I guess
> heating the system with this script is OK ?
>
> Heating the system linearly with weak restraints
> &cntrl
> imin = 0,
> irest = 0,
> ntx = 1,
> ntb = 1,
> taup = 2.0,
> cut = 10,
> ntr = 1,
> ntc = 2,
> ntf = 2,
> tempi = 0.0,
> temp0 = 300.0,
> ntt = 3,
> ig = 2342,
> gamma_ln = 1.0, nmropt = 1,
> nstlim = 50000, dt = 0.002
> ntpr = 100, ntwx = 100, ntwr = 50000
> /
> &wt TYPE='TEMP0', istep1=0, istep2=40000,
> value1=0.1, value2=300.0, /
> &wt TYPE='DUMPFREQ',ISTEP1=10, /
> &wt TYPE='END' /
> Keep protein fixed
> 5.0
> RES 1 367
> RES 385 410
> END
> END
>

‚ÄčThat would work, but ntwx == 100 is a very low number of steps between
trajectory writes. I generally use a value much larger (like ~1000).

I'm not sure what you expect the DUMPFREQ &wt to do. That's usually
reserved for harmonic restraints, which you're not using.

HTH,
Jason
‚Äč
-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Aug 12 2014 - 09:30:02 PDT
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