[gmx-users] MD after equilibration phase
Mark Abraham
Mark.Abraham at anu.edu.au
Fri Apr 6 16:18:30 CEST 2012
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 <jalemkul at vt.edu
> <mailto: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.
>
> -Justin
>
> On Fri, Apr 6, 2012 at 12:42, Peter C. Lai <pcl at uab.edu
> <mailto:pcl at uab.edu> <mailto: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> <mailto:pcl at uab.edu
> <mailto:pcl at uab.edu>> | Birmingham AL
>
> 35294-4461
> (205) 690-0808 |
>
> ==================================================================
>
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>
> --
> -----------------------
> /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 <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>
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> --
> -----------------------
> /Regards,/
> Bipin Singh
>
>
>
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