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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Received on Tue Oct 20 2009 - 18:00:02 PDT
