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.
________________________________________________________________________
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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