[gmx-users] energyfile questions

[Justin A. Lemkul]

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: matteus.lindgren at chem.umu.se <mailto:barbara.addario at chem.umu.se>
> 
>  
> 
> 
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-- 
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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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