Please check with these scripts from heating till MD.
Heating
Heating Step of MMP3 (MMMM): stage-5
&cntrl
imin= 0,
irest=1,
NTX=1,
ntb= 1,
NTPR=500,
NTWX=500,
NTWR=500,
ntr=1,
Tempi=0.0,
Temp0=300.0,
NTT=3,
gamma_ln=1.0,
NTC=2,
NTF=2,
cut= 12.0,
nstlim=2500,
dt=0.002,
/
Keep Protein and inhibitor fixed with weak restraints
10.0
RES 1 557
END
END
Equilibration
Equilibration Step of MMP3 (MMMM): stage-1
&cntrl
imin= 0,
irest=1,
NTX=7,
ntb=2,
ntp=1,
PRES0=1.0,
TAUP=2.0,
NTPR=500,
NTWX=500,
ntr=0,
Tempi=300.0,
Temp0=300.0,
NTT=3,
gamma_ln=1.0,
NTC=2,
NTF=2,
cut=12.0,
nstlim=250000,
dt=0.002
/
Production
Equilibration Step of MMP3 (MMMM): stage-1
&cntrl
imin= 0,
irest=0,
ig=-1,
NTX=7,
ntb=2,
ntp=1,
PRES0=1.0,
TAUP=2.0,
NTPR=500,
NTWX=500,
ntr=0,
Tempi=300.0,
Temp0=300.0,
NTT=3,
gamma_ln=1.0,
NTC=2,
NTF=2,
cut=12.0,
nstlim=2500000,
dt=0.002
/
If you need minimization scripts let me know. But I am sure it is fine.
Just run all these scripts usng PMEMD GPU. It works fine.
On Mon, Jun 9, 2014 at 10:34 AM, James Starlight <jmsstarlight.gmail.com>
wrote:
> also please suggest me where in input file I should provide exactly box
> type used for the simulation. I had the problems with the rectangular boxes
> (not with the cubic) in spite of usage of ntp=3 with constant surface
> tension.
>
> James
>
>
> 2014-06-09 12:17 GMT+04:00 James Starlight <jmsstarlight.gmail.com>:
>
> > Dear Amber users!
> >
> >
> > I've faced with the problems during equilibration of my protein using
> > pmemd.cuda
> >
> > 1- I've started to heat my protein in nvt and quickly obtained
> >
> > ERROR: Calculation halted. Periodic box dimensions have changed too much
> > from their initial values.
> > Your system density has likely changed by a large amount, probably from
> > starting the simulation from a structure a long way from equilibrium.
> >
> > [Although this error can also occur if the simulation has blown up for
> > some reason]
> >
> > The GPU code does not automatically reorganize grid cells and thus you
> > will need to restart the calculation from the previous restart file.
> > This will generate new grid cells and allow the calculation to
> continue.
> > It may be necessary to repeat this restarting multiple times if your
> > system
> > is a long way from an equilibrated density.
> >
> > Alternatively you can run with the CPU code until the density has
> > converged
> > and then switch back to the GPU code.
> >
> > visualization show me that individual water have been moved towards the
> > box boundaries being separated from the rest of the solvent.
> >
> > What would be best solution here
> >
> > 1- Switch to the sander and perform all equilibration using cpu
> >
> > 2- Do equilibration using cuda starting in NPT (with frozen protein) with
> > applied barostat preventing such density artifacts ?
> >
> > James
> >
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>
--
Thanks & Regards;
Soumendranath Bhakat
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Received on Mon Jun 09 2014 - 02:30:02 PDT
