[gmx-users] Problem with continuation of simulation

David van der Spoel spoel at xray.bmc.uu.se
Tue Jun 6 11:55:22 CEST 2006

Sridhar Acharya wrote:
> Hello,
> I had carried out a 20ns protein simulation on Gromacs v3.2.1. Later I 
> continued the simulation on Gromacs v3.3.
> I ran the following command supplying the energy file and trajectory 
> file. But the program gave error and stopped (log message is given below).
> Since I read that supply of energy file is not absolutely required. I 
> again ran tpbconv without -e option for another 10ns. This time the 
> program ran with the warning message that the continuation will not be 
> exact.
> "WARNING: The simulation uses pressure and/or Nose-Hoover temperature 
> coupling,
>         the continuation will only be exact when an energy file is 
> supplied".
> When I plotted the trajectory of the Potential energy, I found the 
> difference, with PE much below than the previous simulation (PE dropped 
> from -559000 to -561000). Can I use the data of this additional 
> simulation, or is it a drastic variation, that I need to take care of?
> Thank you,
> expecting your suggessions.
It is not a good idea to change gromacs versions within a project. 
Obviously in trying to improve the software we fix the bugs that are 
found, and some of these may influence the results. You probably should 
finish your project in 3.2.1 and start using 3.3.1 for your next 
project. Check the website for the differences between the versions of 
the code.

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://folding.bmc.uu.se

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