[gmx-users] Wrong pressure with "mdrun -rerun" option
lulanyuan at msn.com
Fri Jul 24 05:23:27 CEST 2009
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
----- Original Message -----
From: "Mark Abraham" <Mark.Abraham at anu.edu.au>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
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
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