Dear Dr.Justin Thank you for your complete explanation. Please let me discribe where is NPT.cpt comes from:
Before doing Pulling step,I did an NPT step (as your tutorial) to generate NPT ensemble. the outputs of this step were NPT.cpt, NPT.gro and NPT.enr and ... Then I used NPT.gro for Pulling step to generate config0.gro and ... After this step I used the NPT.cpt and config0.gro and .... to generate umbrella0.tpr with grompp. I think it is obvious now ,where is NPT.cpt come from! I think my mistake is as you noted.I didn't use any -t option in grompp,Then I lost the information for npt ensemble. What do you think Thanks in advance for your reply On Sun, May 8, 2011 at 7:03 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > mohsen ramezanpour wrote: > >> 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 where does NPT.cpt come from? Presumably, if you have this file, you > did some equilibration. I don't understand what you've done. If you want > to rely on previous, equilibrium dynamics under an NPT ensemble, you must do > equilibrium MD (not steered) for each configuration under the desired > conditions, then pass the .cpt file to grompp -t when building the umbrella > sampling input files. > > > Then when I use that in grompp for each windows ,I expect the same >> characteristics of system as before(At least the same T)! >> >> > With "gen_vel = no" and no record of the prior state, this is not a > reasonable expectation. You will get a temperature based on the initial > forces present in the system (which determine initial velocities). The > resulting temperature may or may not be identical to the previous state, but > under the influence of a thermostat, you will reach the desired temperature. > > If you're attempting to follow my tutorial directly, at this point I think > you should stop and consider the discussion I have in the tutorial on > maintaining the ensemble: > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/06_umbrella.html > > In the example system (one I know very well), it was satisfactory to simply > use > "gen_vel = no" and allow these initial forces to govern the resulting > dynamics. In many other cases (probably most), you should: > > 1. Generate your configurations (SMD, etc) > 2. Run individual NPT simulations (or whatever ensemble) for each desired > starting configuration (and thus obtain npt0.cpt, npt1.cpt, etc) > 3. Initiate umbrella sampling windows using the npt*.cpt files from each > window. > > Otherwise, skip step 2, use "gen_vel = yes" and discard the first few > hundred ps as equilibration in each window. > > > 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? >> > > These commands do not necessarily preserve the ensemble. Without providing > suitable information to grompp -t, the initial state is lost. I still don't > know where NPT.cpt comes from. You say you're running grompp immediately > after pulling, which is a non-equilibrium ensemble that you don't want to > preserve as input into umbrella sampling. That, and likely the settings in > SMD vs. US are different, so if NPT.cpt corresponds to your SMD simulation, > you probably don't want to be using that for all your umbrella sampling > windows, as the information it contains is for one single snapshot somewhere > along the SMD run. If this is not the case, and you've generated NPT.cpt in > some other manner, you will have to explain where it came from. > > > What do you think if I use NPT.enr OR NPT.trr OR in >> grompp(especially NPT.enr) ? >> > > Not necessary. Using .cpt files is more accurate. > > > Because all of information about NPT step are included in this files. >> >> > Note entirely. The differences between using .edr + .trr vs. .cpt alone > are very small, but using a .cpt file is the most rigorously correct way to > maintain the ensemble. > > -Justin > > Thanks in advance for your >> >> On Sun, May 8, 2011 at 5:47 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> 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 <http://vt.edu> | (540) 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> > -- > ======================================== > > 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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