[gmx-users] Restart dmpc membrane

[David van der Spoel]

On Tue, 2004-06-01 at 16:11, Carl-Johan Högberg wrote:
> Thats true but in  tpbconv i use the .tpr file i used when i originally 
> started the simulation. When i created this .tpr with grompp i used an 
> .mdp file. Or should i use grompp to create a new .tpr file before i use 
> tpbconv?
No.

the first time you run grompp, grompp generates the velocities. mdrun
just reads them from the tpr. with tpbconv you will get the last
velocities from your trajectory.
> 
> Carl-Johan
> 
> 
> David van der Spoel wrote:
> 
> >On Tue, 2004-06-01 at 14:11, Carl-Johan Högberg wrote:
> >  
> >
> >>Ok it seems to work! Thanks.
> >>
> >>Another question. In my .mdp file i have the option:
> >>
> >>gen_vel = yes
> >>
> >>When i restart my simulation with tpbconv do i get new velocities or 
> >>does the simulation continue with the velocities in the .gro or .trr file?
> >>
> >>    
> >>
> >If you use tpbconv you don't use an mdp file.
> >
> >
> >  
> >
> >>Best regards
> >>Carl-Johan
> >>
> >>
> >>
> >>David van der Spoel wrote:
> >>
> >>    
> >>
> >>>On Tue, 2004-06-01 at 12:38, Carl-Johan Högberg wrote:
> >>> 
> >>>
> >>>      
> >>>
> >>>>Hi gmx-users
> >>>>
> >>>>I have some problems restarting a dmpc membrane simulation. The 
> >>>>simulation has been running for 30ns and now a want to start it again. 
> >>>>When using tpbconv i get the following error:
> >>>>
> >>>>WARNING: The simulation uses pressure and/or temperature coupling,
> >>>>        the continuation will only be exact when an energy file is supplied
> >>>>
> >>>>And also:
> >>>>
> >>>>0 steps (0 ps) remaining from first run.
> >>>>You've simulated long enough. Not writing tpr file
> >>>>
> >>>>Anybody who has any suggestions how to solve this problem?
> >>>>   
> >>>>
> >>>>        
> >>>>
> >>>tpbconv -f -s -e -o -extend 1000
> >>> 
> >>>
> >>>      
> >>>
> >>>>Best regards
> >>>>Carl-Johan
> >>>>   
> >>>>
> >>>>        
> >>>>
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone:  +46 18 471 4205  fax: +46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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