Matteus Lindgren wrote:
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.
What does gmxcheck show you about the spacing of the frames? That to me sounds
very uneven, like something went wrong.
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?
Again, something is very wrong with the .edr file. You should never have to
manually hack out frames. Can you guarantee that the frame you are using
corresponds to the time you think it does? What was the command line you used
with tpbconv?
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?
Small groups are prone to larger fluctuations, which in and of itself may not be
a problem. Coupling the whole system to the same thermostat often gives rise to
the "hot solvent/cold solute" issue, which I know for sure is the case with
Berendsen, and I believe is also problematic in other thermostats as well.
-Justin
Regards
/Matteus
Matteus Lindgren
Graduate student
Department of Chemistry
Umeå University
SE-901 87 Umeå, Sweden
Tel: +46 (0)90 786 53 68
e-mail: [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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