[gmx-users] mdrun -rerun question
Michael Shirts
mrshirts at stanford.edu
Tue Dec 16 10:47:01 CET 2003
I'm trying to understand what the -rerun option does exactly.
So, here's my problem. I ran mdrun, outputting a .trr with coordinates every
500 steps (0.002 ps step length, 100 ps total). I then used g_energy and the
.edr file to generate an .xvg with a number of observables (listed below). I
then ran a mdrun -rerun using the output .trr file, generating a new .edr
file, and a new .xvg. All programs were run complied in double precision. I
then took the difference between the numbers in the two files, and got the
following results. Why any difference? Shouldn't it produce the same
energies?
Some particularly odd things -- why is the box length different between the
two .edrs? If it's just taking snapshots, the box should be the same at every
step. Instead, there's a difference. Secondly, the differences are multiples
of the same number, which is some negative power of two. For example, in the
LJ energy column, all energies are different by multiples of 1/2048. In the
short range coulomb column, the multiples appear to be of 1/512 (I'm just
giving the first 20 here - I generated 100 ps worth). Only the box length
(and therefore the dispersion correction, which is proportional to the volume,
and the potential energy, which includes the dispcorr) isn't following this
pattern. Is this an artifact of the .edr format? If so, why is it appearing
at such a low resolution? The total LJ energy is approximately 6000 kJ/mol,
so these errors are of order 10^-6 or 10^-7, much too low for double
precision. And why is it different, if it's going through the same energy
routines? I guess I could understnd some sort of rounding error for the
energies, but the box size error is of order 10^-4; a box problem I might
account for the energy differences, too, as the total energies would change as
the periodic boundary conditions change.
Any suggestions?
Also, the "averages" output of g_energy from a rerun file are incorrect, as
they appear to have the numerator of the coordinate output frequency, but the
denominator of the original run, giving incorrect averages for these
snapshops.
Thanks,
Michael Shirts
Differences between .edr's
time(ps) LJ(SR) DispCorr Coulomb(S) Coulomb(L) Potential Box-X
0.00000 0.004394 0.000030 -0.007813 0.000000 0.000000 0.000000
1.00000 0.000000 -0.090805 -0.003907 -0.000976 -0.089844 -0.000357
2.00000 -0.001953 -0.004547 -0.001953 -0.000976 -0.007812 -0.000018
3.00000 -0.001465 -0.064651 0.005859 0.000976 -0.062500 -0.000265
4.00000 -0.003907 0.104446 0.000000 -0.000976 0.121093 0.000409
5.00000 0.003418 0.174408 -0.003906 0.000977 0.175781 0.000675
6.00000 -0.003418 0.029098 0.001953 0.000000 0.027344 0.000115
7.00000 0.001953 0.077423 -0.001953 0.000976 0.078125 0.000307
8.00000 0.000488 -0.055603 -0.001953 0.000000 -0.054687 -0.000223
9.00000 0.002441 0.052551 0.000000 0.000976 0.054687 0.000207
10.00000 0.000000 -0.132507 -0.003906 0.000000 -0.113282 -0.000518
11.00000 -0.001953 0.001907 0.007812 0.000976 0.007813 0.000008
12.00000 -0.001953 -0.029938 0.003906 0.000000 -0.027343 -0.000122
13.00000 -0.004883 -0.017075 0.000000 0.000000 -0.019531 -0.000067
14.00000 -0.003906 -0.049790 0.000000 0.000000 -0.050781 -0.000196
15.00000 -0.003418 0.042145 0.007812 0.001953 0.046875 0.000168
16.00000 0.002930 0.065643 0.000000 0.000976 0.070313 0.000260
17.00000 0.003418 0.003525 -0.001953 -0.000976 0.007812 0.000014
18.00000 0.004394 0.092026 -0.003907 0.000000 0.093750 0.000371
19.00000 -0.001464 -0.082428 0.003907 0.000977 -0.078125 -0.000327
20.00000 -0.000489 -0.103592 -0.003907 -0.000976 -0.105469 -0.000410
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