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 |
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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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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