AMBER Archive (2009)

Subject: [AMBER] amber8 pmemd trajectory coordinates problem

From: wong105_at_llnl.gov
Date: Tue Oct 20 2009 - 19:32:24 CDT

Dear Amber users;

     I ran an explicit water simulation (TIP3P, PBC, counter ions,
pme, etc) using PMEMD version 8. The problem is that when I visualize
the trajectory it seems to advance very little except every 4th
trajectory step. The system is of medium size ( 48732 Atoms) and my
input file is below:

  &cntrl
    imin = 0,
    ntx=5,
    irest=1,
    ntpr = 5000,
    ntwx = 5000,
    iwrap=1,
    ntwr = 5000,
    nstlim =1000000,
    dt = 0.001,
    ntb = 1,
    cut = 12,
    ntr = 0,
    ntc = 2,
    ntf = 2,
    ntt = 1,
    temp0 = 300.0,
    nrespa=4,
  &end

To illustrate what I mean, I ran a rms fit to C-alphas analysis using
ptraj. The output is below. I placed stars at positions where the
C-alpha rmsd changed significantly from the previous.

     4.00 0.82920
     5.00 0.82906
     6.00 0.82890
     7.00 0.82872
     8.00 0.82843
     9.00 0.82844
    10.00 0.82839
    11.00 0.82832
    12.00 0.86168 *****
    13.00 0.86181
    14.00 0.86193
    15.00 0.86208
    16.00 0.91274 *****
    17.00 0.91281
    18.00 0.91294
    19.00 0.91309
    20.00 1.06776 *****
    21.00 1.06770
    22.00 1.06768
    23.00 1.06790
    24.00 1.01943 *****
    25.00 1.01924
    26.00 1.01909
    27.00 1.01896
    28.00 0.83520 *****
    29.00 0.83459
    30.00 0.83395
    31.00 0.83331
    32.00 1.04453 *****
    33.00 1.04468

This occurred for simulations of 4 different systems. In addition,
running on the Amber 10 version of PMEMD, this problem disappears.
While that's a solution for future simulations, I wonder if I can
salvage any of the data in these trajectories. Can I simply use every
4th snapshot for analysis, for example? Any ideas would be greatly
appreciated.

Thanks;
-Sergio

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