[gmx-users] Umberella sampling
ramezanpour.mohsen at gmail.com
Sun May 8 16:04:07 CEST 2011
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
>> 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:
> It is the average that is most meaningful.
> 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
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