Dear Jason,
Thanks for the prompt answer. We found this behaviour even in systems with extremely low water concentration. Could this happen because carbohydrates incompressibility is also very large?
Regards,
Hernán
> Date: Thu, 22 Sep 2011 22:49:14 -0400
> From: jason.swails.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] Large pressure fluctuations over the whole run
>
> Large pressure fluctuations are expected due to the fact that water is
> largely incompressible. The metric you want to look at here is density if
> you're looking for proper pressure equilibration, not so much pressure.
>
> HTH,
> Jason
>
> On Thu, Sep 22, 2011 at 7:14 PM, Hernán Meier <hmeier.hotmail.com.ar> wrote:
>
> >
> >
> > Dear Amber users:
> >
> > We are doing MD calculations with Amber 11 and sander.mpi on a quaternary
> > system (disaccharides + 1 amino-acid + water) with PBC in order to study
> > transport properties.
> >
> > We did a 20.000 steps minimization combining Steepest Descent and Conjugate
> > Gradient first keeping restrains and then 50.000 steps with the same combine
> > methods without any restrain.
> >
> > After that we did a 50 ps constant volume MD with the same restrictions
> > used during the minimization. Then we released the restrictions and followed
> > the MD at constant pressure in several 500ps runs.
> >
> > We found that at the first run (of 500 ps) the average pressure lead to a
> > high value. In the following runs this value rise fluctuating between 0.6 -
> > 1.7 (the average) this value don't reach 1 even after 50 ns of running.
> >
> > Here are the inputs:
> >
> > Could anybody suggest us the possible reason for this behaviour, is it
> > normal?
> >
> >
> >
> >
> >
> >
> >
> > at NVT conditions:
> >
> > imin = 0,
> > irest = 0,
> > ntx = 1,
> > ntb = 1,
> > cut = 8,
> > ntr = 1,
> > ntc = 2,
> > ntf = 2,
> > tempi = 0.0,
> > temp0 = 300,
> > ntt = 3,
> > gamma_ln = 2.0,
> > nstlim = 25000, dt = 0.002,
> > ntpr = 100, ntwx = 100, ntwr = 1000
> >
> > /
> >
> > 10.0
> > RES 145 170
> > END
> > END
> >
> >
> >
> >
> >
> >
> > at NTP conditions:
> >
> >
> >
> >
> > imin = 0, irest = 1, ntx = 5,
> > ntb = 2, pres0 = 1.0, ntp = 1,
> > taup = 2.0,
> > cut = 10, ntr = 0,
> > ntc = 2, ntf = 2,
> > tempi = 300.0, temp0 = 300.0,
> > ntt = 3, ig = -1, gamma_ln = 2.0,
> > nstlim = 250000, dt = 0.002,
> > ntpr = 500, ntwx = 500, ntwr = 5000
> >
> > Waiting for a reply.
> > Regards,
> > Hernán Meier from Quitex Group UTN FRRe, Argentina
> >
> >
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Mon Sep 26 2011 - 15:30:02 PDT
