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

--
========================================

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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