[gmx-users] MD after equilibration phase
bipinelmat at gmail.com
Fri Apr 6 15:34:10 CEST 2012
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....
On Fri, Apr 6, 2012 at 12:42, Peter C. Lai <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
> > conditions wich are equal to the last equilibration phase ( e.g often
> > 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
> > 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
> > 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
> > .cpt file and from wich source the velocities from equilibration phase
> > 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
> cpt file or you can specify the previous .trr and it will take the last
> 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 | Birmingham AL 35294-4461
> (205) 690-0808 |
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