[gmx-users] Simulations in vacuo

Erik Marklund erikm at xray.bmc.uu.se
Wed Jan 12 11:40:09 CET 2011

Zoe Hall skrev 2011-01-11 16.29:
> Hi gmx-users,
> I am trying to set up a simulation of a large protein /in vacuo/ using 
> the OPLS-AA forcefield, with conditions based on Patriksson et. al 
> (Biochemistry 2007, 46 p933).  Basically after energy minimisation, 
> the protein is run for 10ps in vacuum with constant temperature at 
> 300K. This is followed by the full production run of 10ns with 
> temperature and pressure coupling turned off, H bonds are constrained 
> using SHAKE with tolerance 0.001. For vacuum conditions, the periodic 
> boundary conditions are turned off, and no cut-offs are used whatsoever.
> I am not sure, however, what is the appropriate choice for 
> "coulombtype" and other electrostatic parameters for vacuum 
> simulations. I have set "epsilon_r" to 2, as this seems to be an 
> accepted value for proteins but if anyone has comments on this, I 
> would appreciate it.
> Thanks very much,
> Zoe
> Zoe Hall
> Department of Chemistry
> Oxford University
> _zoe.hall at chem.ox.ac.uk_
I should point out that there is probably an error in the methods 
section. If I recall correctly we used a 0.5 fs timestep. We couldn't 
get good conservation of total energy with 1 fs steps. Remember to use 
double precision, or you will again loose conservation of total erergy. 
Remember to monitor the total energy, because if it's drifting you need 
to have a more conservative setup, e.g., use a smaller timestep.

Take a look at our "follow up" study (Marklund et. al., PCCP (2009) 11 
p. 8069--8078) where we used LINCS and managed to conserve the total 
energy with a 1 fs time step.

Good luck!

Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/

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