[gmx-users] Umberella sampling

mohsen ramezanpour ramezanpour.mohsen at gmail.com
Sun May 8 16:04:07 CEST 2011

Dear Dr.Justin

I didn't any equilibration for any windows! Because:
As I know the thermodynamics of the system had wroten in NPT.cpt file (for
example the velocities and etc).
Then when I use that  in grompp for each windows ,I expect  the same
characteristics of system as before(At least the same T)!

Actually after PULLING step I used the following commands:
grompp  -f  umbrella.mdp   -c   config0.gro  -p  complex.top  -o
umbrella0.tpr  -n index.ndx

mdrun  -v  -deffnm  umbrella0    -px  pullx0.xvg   -pf   pullf0.xvg   -cpi

what is your point of view now?
What do you think if I use NPT.enr  OR   NPT.trr   OR   in
grompp(especially  NPT.enr) ?
Because all of information about NPT step are included in this files.

Thanks in advance for your

On Sun, May 8, 2011 at 5:47 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> 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
> 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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