When we mention gen_vel=no ;And provide pdb as input with no velocities As mentioned in the manual: "The velocities are set to zero when there are no velocities in the input structure file"
Please elaborate what does this sentence mean. On Fri, Apr 6, 2012 at 19:10, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > bipin singh wrote: > >> Also, if we give continuation=yes in mdp file and use input as pdb file >> as input instead of gro file, grompp never complains....I don't no how it >> reads velocities from pdb file (as no velocities are present in pdb files). >> Ideally it should complain that no velocities found in input file.... >> >> > Again, the "continuation" keyword has nothing to do with velocities. If > you have "gen_vel = no" and you provide a .pdb file with no velocities, > then you do not preserve velocity information. Whatever the initial forces > are govern the resulting motions. In any case, you do not preserve the > previous simulation conditions. > > -Justin > > On Fri, Apr 6, 2012 at 12:42, Peter C. Lai <p...@uab.edu <mailto: >> p...@uab.edu>> wrote: >> >> On 2012-04-06 11:05:51AM +0400, James Starlight wrote: >> > Dear Gromacs users! >> > >> > >> > I have small question about order of the runs and input data. >> > >> > Ussually I do 2 equilibration phases and subsequent productive >> phase in the >> > conditions wich are equal to the last equilibration phase ( e.g >> often this >> > is npt ). >> > >> > In the second equil.mdp and md.mdp there is option >> > >> > continuation = yes >> > >> > which means that there have been previous phases of the >> simulation from >> > wich coordinates and velocities should be taken. >> > >> > As I understood the coordinates is taken from .gro file but from >> what file >> > the velocities must be providen ? Does it .cpt checkpoint file from >> > previous run? In some cases I've forgotten to define -t npt.cpt >> for my MD >> > run providing only coordinates in GRO file, topology and md.mdp >> but I have >> > not seen any errors in such simulation due to absence of that >> .cpt and >> > GROMPP never remind me of the absense of this file. What exactly >> is in that >> > .cpt file and from wich source the velocities from equilibration >> phase are >> > taken ? >> >> continuation = yes is telling LINCS that it is a continuation and >> it should not attempt to refit the constrained bonds on the first pass. >> >> The coords, velocities, state, and box information are taken either >> from the >> cpt file or you can specify the previous .trr and it will take the >> last frame >> from that and use it. If you used the output gro file without -t, then >> it will take coordinates and velocities from the .gro but the >> problem there >> is the limited precision (3 decimal points for each). >> >> -- >> ==============================**==============================**====== >> Peter C. Lai | University of Alabama-Birmingham >> Programmer/Analyst | KAUL 752A >> Genetics, Div. of Research | 705 South 20th Street >> p...@uab.edu <mailto:p...@uab.edu> | Birmingham AL >> >> 35294-4461 >> (205) 690-0808 | >> ==============================**==============================**====== >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> >> >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> Please search the archive at >> >> http://www.gromacs.org/**Support/Mailing_Lists/Search<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-request@**gromacs.org<gmx-users-requ...@gromacs.org> >> >. >> >> Can't post? Read >> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> >> >> >> >> -- >> ----------------------- >> /Regards,/ >> Bipin Singh >> >> > -- > ==============================**========== > > 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<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- ----------------------- *Regards,* Bipin Singh
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