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 <jalem...@vt.edu
<mailto:jalem...@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 <p...@uab.edu
<mailto:p...@uab.edu> <mailto: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> <mailto: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 <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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