[gmx-users] MD after equilibration phase
bipinelmat at gmail.com
Fri Apr 6 16:15:19 CEST 2012
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
Please elaborate what does this sentence mean.
On Fri, Apr 6, 2012 at 19:10, Justin A. Lemkul <jalemkul at 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.
> On Fri, Apr 6, 2012 at 12:42, Peter C. Lai <pcl at uab.edu <mailto:
>> pcl at 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
>> pcl at uab.edu <mailto:pcl at uab.edu> | Birmingham AL
>> (205) 690-0808 |
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>> 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
> gmx-users mailing list gmx-users at gromacs.org
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