bipin singh wrote:
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.
No. Velocities are only saved in the .trr and/or .cpt files. There is no place
for velocities in .pdb files.
-Justin
On Fri, Apr 6, 2012 at 19:48, Mark Abraham <[email protected]
<mailto:[email protected]>> 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 <[email protected]
<mailto:[email protected]>> 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 <[email protected]
<mailto:[email protected]> <mailto:[email protected]
<mailto:[email protected]>>> 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
[email protected] <mailto:[email protected]> <mailto:[email protected]
<mailto:[email protected]>> | 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
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--
========================================
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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