Thanks for your comments. One more question. Does Gromacs saves velocities in pdb files, when we use gen_vel=yes option in mdp and save the output(-c) of mdrun as pdb file instead of gro file.
On Fri, Apr 6, 2012 at 19:48, Mark Abraham <mark.abra...@anu.edu.au> wrote: > On 7/04/2012 12:15 AM, bipin singh wrote: > > 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. > > > Each atom must have a velocity in a *dynamical* simulation. If there is no > instruction for what values to use (i.e. not generated or supplied), zero > is used. Integration proceeds from there, and this may or may not be > stable, and certainly will not have the desired temperature (yet)... > > Mark > > > > 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 >>> 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 >>> >>> >>> >>> >>> -- >>> ----------------------- >>> /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 >> >> >> ======================================== >> -- >> 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 >> > > > > -- > ----------------------- > *Regards,* > Bipin Singh > > > > > > -- > 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 > -- ----------------------- *Regards,* Bipin Singh
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