[gmx-users] box size with pressure coupling

Lynne E. Bilston bilston at aeromech.usyd.edu.au
Thu Feb 14 23:15:18 CET 2002

Hi all,

Maybe I'm missing something obvious here, if so please enlighten me.

I'm doing some pressure coupled simulations of a lipid/protein combination, 
starting with the usual em, then pr runs.  I follow that with a bit of 
equilibration with no restraints, using pressure coupling to zero pressure, 
to let the box size come to some equilibrium state. That's all fine. Then I 
use the output from that run to start another pressure coupled run, this 
time a semiisotropic pressure coupled run.

The weird thing is that despite using the coordinates (-c pdb file) and the 
trajectory ( -t trr file) from after the  equilibration, the box size at 
the start of the second pressure coupled run resets itself to the size 
before the original pressure coupled run. Is grompp taking the coordinates 
(and thus box size) somehow from the first frame of the trajectory instead 
of the last as specified in the manual?  To summarise, I am doing the 

1. em (OK)
2. pr (OK)
3. equilibration - md with isotropic pressure coupling, p=0 (runs OK)
4. md with semi-isotropic pressure coupling, resets box size at the start 
of the simulation to size after step 2.

I checked that the box size is correct in the pdb file I'm using as input 
for grompp in step 4, so I guess it must be getting the initial coordinates 
and size from the trajectory file, not the finishing coordinates?? This 
only seems to happen when I use the trajectory option, not the coordinates 
file alone. I just wanted to keep the velocities etc.

Any suggestions?



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