Yes, I've just run the same but with monte carlo barostat in production run.
As I've realized problem was exactly in the rectangular box because when
I've switched to the truncated octahedral problem my simulation have been
stable during both production and equilibration.
James
2014-06-09 13:15 GMT+04:00 Soumendranath Bhakat <
bhakatsoumendranath.gmail.com>:
> 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
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Thanks & Regards;
> Soumendranath Bhakat
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 09 2014 - 03:30:02 PDT
