[gmx-users] Wrong pressure with "mdrun -rerun" option

Lanyuan Lu lulanyuan at msn.com
Fri Jul 24 05:23:27 CEST 2009

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 

----- 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
> pressures?
> Mark
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