AMBER Archive (2003)

Subject: Re: AMBER: Pressure during MD

From: Joćo Barroso (joao.barroso_at_ibmb.uib.no)
Date: Mon Nov 17 2003 - 03:36:41 CST

Hi,

Thank you for your answer. Here's the input file:

  &cntrl

    nstlim=5000000,
ntt=1,
    scee=1.2,
ntwe=5000,
    ntpr=5000,
ntwx=5000,
    vlimit=10,

  &end

  &wt TYPE='TEMP0', istep1=0, istep2=10000, value1=0,
value2=300,
  &end

  &wt TYPE='TEMP0', istep1=10001, istep2=5000000, value1=300,
value2=300,
  &end

  &wt TYPE='TAUTP', istep1=0, istep2=10000, value1=0.2,
value2=0.2,
  &end

  &wt TYPE='TAUTP', istep1=10001, istep2=5000000, value1=2.0,
value2=2.0,
  &end

  &wt TYPE='NTB', istep1=0, istep2=10000, value1=1,
value2=1,
  &end

  &wt TYPE='NTB', istep1=10001, istep2=5000000, value1=2,
value2=2,
  &end

  &wt TYPE='NTP', istep1=0, istep2=10000, value1=0,
value2=0,
  &end

  &wt TYPE='NTP', istep1=10001, istep2=5000000, value1=1,
value2=1,
  &end

  &wt
TYPE='END'
  &end

The control data for the run in the mdout reads:

General flags:
      imin = 0, nmropt = 0

Nature and format of input:
      ntx = 1, irest = 0, ntrx = 1

Nature and format of output:
      ntxo = 1, ntpr = 5000, ntrx = 1,
ntwr = 500
      iwrap = 0, ntwx = 5000, ntwv = 0,
ntwe = 5000
      ioutfm = 0, ntwprt = 0, idecomp = 0,
rbornstat= 0

Potential function:
      ntf = 1, ntb = 1, igb = 0,
nsnb = 25
      ipol = 0, gbsa = 0
      dielc = 1.00000, cut = 8.00000, intdiel = 1.00000
      scnb = 2.00000, scee = 1.20000

Frozen or restrained atoms:
      ibelly = 0, ntr = 0

Molecular dynamics:
      nstlim = 5000000, nscm = 1000, nrespa = 1
      t = 0.00000, dt = 0.00100, vlimit = 10.00000

Temperature regulation:
      ig = 71277, ntt = 1, vrand = 0
      temp0 = 300.00000, tempi = 0.00000, heat = 0.00000
      dtemp = 5.00000, tautp = 1.00000

Ewald parameters:
      verbose = 0, ew_type = 0, nbflag = 1, use_pme
= 1
      vdwmeth = 1, eedmeth = 1, frc_int = 0,
netfrc = 1
      Box X = 100.998 Box Y = 59.117 Box Z = 68.898
      Alpha = 90.000 Beta = 90.000 Gamma = 90.000
      NFFT1 = 100 NFFT2 = 60 NFFT3 = 72
      Cutoff= 8.000 Tol =0.100E-04
      Ewald Coefficient = 0.34864
      Interpolation order = 4
| PLEVEL = 1: runmd parallelization, no EKCMR

I hope this helps. I can see that ntb=1 and I can't see any value for ntp
(I guess it's 0) in mdout, but this corresponds to the beginning of the MD,
which starts with equilibration for 10000 steps. However, and according to
the input file, shouldn't it change to constant pressure after this initial
equilibration steps? Once again thank you for your help.

Best regards,
Joao Barroso

At 14:52 16-11-2003 -0800, you wrote:
>On Sun, Nov 16, 2003, Joo Barroso wrote:
> >
> > I'm rather new with Amber, so I have a simple question regarding the
> > pressure of the system during MD. I'm using Amber 7 and a periodic system
> > at 300 K. I'm running first equilibration at constant volume (ntb=1 and
> > ntp=0), and I change to constant pressure for the MD (ntb=2 and ntp=1). I
> > didn't give any value for "press0", assuming that it would be the default
> > value of 1 atm. However, in each step the output file reads
> press=0.0 both
> > in equilibration and the remaining simulation (see example below).
> Should I
> > be concerned about this? Is the system running at 1 atm or do I have to
> > specify the pressure in the input file?
> >
> > NSTEP =1365000 TIME(PS) = 1365.000 TEMP(K) = 299.63 PRESS = 0.0
> > Etot = -63273.9308 EKtot = 26416.5302 EPtot = -89690.4610
> > BOND = 15843.0623 ANGLE = 3334.9801 DIHED = 2305.3420
> > 1-4 NB = 1430.4541 1-4 EEL = 10987.8157 VDWAALS = 11638.1704
> > EELEC = -135230.2857 EHBOND = 0.0000 RESTRAINT = 0.0000
> > Ewald error estimate: 0.2029E-04
> >
> ------------------------------------------------------------------------------
>
>It really doesn't look like you are doing a constant pressure simulation.
>Double-check the mdout file to be sure that ntb=2 and ntp=1. The default
>pressure is indeed one atmosphere, but you are somehow not getting a pressure
>calculation. Without seeing more about your input or output, I cannot say
>why.
>
>..regards...dac
>
>--
>
>==================================================================
>David A. Case | e-mail: case_at_scripps.edu
>Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
>The Scripps Research Institute | phone: +1-858-784-9768
>10550 N. Torrey Pines Rd. | home page:
>La Jolla CA 92037 USA | http://www.scripps.edu/case
>==================================================================
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