[gmx-users] Umberella sampling

[Justin A. Lemkul]

mohsen ramezanpour wrote:
> Dear Dr.Justin
> 
> Regarding doing umbrella sampling:
> I used gen_vel =no
> and I prefer to use from thermodynamics of system in  NPT.cpt
> 
> Although the T and P were as I did set in NPT.mdp file (T=310 ,P=1 bar)
> But  their values in my umbrela.log files are not as before (for 
> example  P=-8.434578e+1)
> 
> Where did I wrong?

I have no clue.  You didn't provide your commands or any evidence that the prior 
ensemble was to be maintained.  If you have done NPT equilibration in each 
window, then pass the .cpt file to grompp and the ensemble should be preserved 
in each window.  Note that an instantaneous pressure value means nothing, as 
discussed weekly on this list and online:

http://www.gromacs.org/Documentation/Terminology/Pressure

It is the average that is most meaningful.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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