Hi Mark,
Thanks for your reply. Yes, I did save velocities in the same frequency as
positions. And the length of two compared trajectories are exactly the same.
I think I've figured it out and I did looked at the average values as the
output of the g_energy. It seems the number 545.384 from the original MD edr
file is incorrect. I opened the xvg file in xmgrace and found the average
pressure should be 1153.22, which is close to the rerun result. I used the
command "g_energy -f *.edr -o *.xvg" to dump the pressure from two edr files
and found both of the two xvg files have time from 0 ps to 200 ps with 201
frames. I also found for each time step the pressure values are close for
the two files. Therefore, I don't understand why I got the incorrect average
pressure from the original edr output, while the rerun output was correct.
Another test I did was to type "g_energy -f *.edr -o *.xvg -b 100" to get
the last 100 ps results. And this time the average number from the original
edr file is still incorrect. However, just as in the whole 200 ps case, I
can get the right number if I manually calculate the average from the xvg
file.
Lanyuan
----- Original Message -----
From: "Mark Abraham" <[email protected]>
To: "Discussion list for GROMACS users" <[email protected]>
Sent: Thursday, July 23, 2009 7:55 PM
Subject: Re: [gmx-users] Wrong pressure with "mdrun -rerun" option
LuLanyuan wrote:
Hello all,
From the notes for gmx 4.0.5, the pressure and virial from "-rerun"
should be correct. However, I did a test for a box of tip3p water and
found the pressure results from rerun were different compared to the
original results. For the first MD simulation , I simulated it for 200 ps
and use the neighbor list update frequency 1. I used "g_energy" to
extract pressure results and the results were 545.384 and 1153.55 bars
for the MD and rerun, respectively. The gromacs version is 4.0.5.
Did you save velocities suitably? Did your primary mdrun include an
equilibration period that the rerun did not? Are you quoting average
pressures?
Mark
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