AMBER Archive (2006)

Subject: Re: AMBER: Constant pressure - restart - Amber8

From: Jennie Thomas (jenniet_at_uci.edu)
Date: Fri Feb 24 2006 - 14:18:56 CST

Here is the top of my .out file:

# 100 ps const. pressure. / const. temp. equilibration; shake;
polarizability
 &cntrl
    imin = 0,

    ntx = 5, irest = 1,

    ntpr = 100, ntwr = 100, ntwx = 500,
    ntwd = 500,ntwe=100,
    iwrap = 1,

    ntf = 2, ntb = 2,
    cut = 12, ipol = 1,
    max_field = 8.0, switch_fac = 0.9,

    nstlim = 100000, dt = 0.0001, t = 0,

    ntt = 1, temp0 = 300.0, tautp = 1.0,
    ntp = 1, pres0 = 1.0, taup = 1.0,

    ntc = 2, tol = 0.00001,

 &end
 &ewald
      use_pme=1, eedmeth=1, vdwmeth=0
      a=30., b=30., c=35.
      indmeth=1, diptol=0.0001
 &end

--------------------------------------------------------------------------------
   1. RESOURCE USE:
--------------------------------------------------------------------------------

| Flags:
 getting new box info from bottom of inpcrd
| peek_ewald_inpcrd: Box info found
|Largest sphere to fit in unit cell has radius = 15.000
| New format PARM file being parsed.
| Version = 1.000 Date = 01/19/06 Time = 10:16:59
 NATOM = 3022 NTYPES = 5 NBONH = 2592 MBONA = 516
 NTHETH = 0 MTHETA = 1032 NPHIH = 0 MPHIA = 1032
 NHPARM = 0 NPARM = 0 NNB = 4144 NRES = 1036
 NBONA = 516 NTHETA = 1032 NPHIA = 1032 NUMBND = 4
 NUMANG = 3 NPTRA = 1 NATYP = 5 NPHB = 0
 IFBOX = 1 NMXRS = 4 IFCAP = 0 NEXTRA = 0
 NCOPY = 0

The final line of the .restrt file is:
  29.5318870 29.5318870 34.4538682 90.0000000 90.0000000 90.0000000

The file line of the .crd file is:
29.532 29.532 34.454

Here is a plot of the volume (from the .mden file) vs simulation time,
each disconnect in the volume is a restart:
https://webfiles.uci.edu/jenniet/temp/vol.ps

Any thoughts on what is going on?

Cheers,
Jennie

David A. Case wrote:

>On Fri, Feb 24, 2006, Jennie Thomas wrote:
>
>
>
>>I did a restart from a constant pressure run, for some reason the volume
>>of my box was not read in from restart file.
>>
>>
>
>Please post the top part of your output file (up to where the first energies
>are reported.) Generally, what you report is not supposed to happen. There
>should be lines like "getting new box info from bottom of inpcrd", and
>"Box info found". But if we have your output file, we can see all of the
>input and output parameters. It would also be helpful to post the last line
>of the restart file you were using.
>
>...thanks....dac
>
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