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 NPT.cpt 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 <jalem...@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 > 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 > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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