[gmx-users] energyfile questions

Matteus Lindgren matteus.lindgren at chem.umu.se
Thu Sep 4 18:36:30 CEST 2008

Hi all


I apologize if these are boring basic questions but I would really like to
get help with them!


1)      I´m doing NPT MD simulations of protein in water and got somewhat
confused when using tpbconv to restart after the first run. The run is
6million timesteps and nstenergy is set to 250 which I guess should give me
24000 energy outputs to the .edr file. However, my edr file contains 24098
outputs, with an extra output roughly every 58000 timesteps. Why? The log
file and trajectory contains the number of outputs I´ve specified and the
run did not crash or anything.


2)      When restarting with tpbconv I submit the energyfile on the
commandline as well as the .trr file. Tpbconv seems to take the last
coordinates and velocities from the .trr but not the last frame from the
.edr file. This seems to happen also for .edr without the “extra frames”
described above. I have to manually remove all but the last frame from the
.edr to have tpbconv select the energy data from the same time as the
coordinates. Why?


3)      I run Nose-Hoover temperature coupling on the protein and solvent in
separate tc_groups, with a ref_t of 350K and tau_t of 0.5. Looking at the
protein temperature, it fluctuates from 325K to 375K which to me sounds like
a lot, even though the protein is rather small – 100residues. The water
fluctuates roughly 15K . I do get the warning of less than 10% of the atoms
(system size 23000atoms) during grompping. Would it be better to have only
one tc_group?





Matteus Lindgren 

Graduate student 


Department of Chemistry
Umeå University
SE-901 87 Umeå, Sweden
Tel: +46 (0)90 786 53 68
e-mail:  <mailto:barbara.addario at chem.umu.se> matteus.lindgren at chem.umu.se


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