The problem was solved by adding -pbc mol -ur compact flags to the trjconv.
So the problems were indeed in pbc conditions
James
2013/5/3 Mark Abraham
> On Fri, May 3, 2013 at 3:17 PM, James Starlight >wrote:
>
> > Mark,
> >
> >
> > but if I run npt equilibration onto minimized structure (with
On Fri, May 3, 2013 at 3:17 PM, James Starlight wrote:
> Mark,
>
>
> but if I run npt equilibration onto minimized structure (without
> velocities) without definition of the new velocities in the npt.mdp file
>
> gen_vel = No
>
> I noticed that in npt.gro file velocities present. Have it been ass
Mark,
but if I run npt equilibration onto minimized structure (without
velocities) without definition of the new velocities in the npt.mdp file
gen_vel = No
I noticed that in npt.gro file velocities present. Have it been assigned
inspite on
gen_vel = No in mdp?
James
2013/5/3 Mark Abraham
EM has no velocities, by definition. Does the EM mdrun write a .gro file
with velocities? If so, that's a bug.
On Fri, May 3, 2013 at 2:51 PM, James Starlight wrote:
> I've noticed that the minimized conformers no longer has the velocities in
> gro file (and npt rus without warnings in that case
I've noticed that the minimized conformers no longer has the velocities in
gro file (and npt rus without warnings in that case) in comparison to the
not-minimized structures ( where velocities were present and gromp sent
warnings). All pbc options lare the same for all conformers and box vectors
co
On Fri, May 3, 2013 at 11:15 AM, James Starlight wrote:
> Mark,
>
> thanks for suggestions
>
> as I've told previously I've removed pbc via trjconv witout -pbc mol and
> -pbc
> nojump flags
I didn't see anything like that in this thread...
> (the same way I found in Justin's umbrella tutorial
Mark,
thanks for suggestions
as I've told previously I've removed pbc via trjconv witout -pbc mol and -pbc
nojump flags (the same way I found in Justin's umbrella tutorial where
conformers were extracted from pulling trajectory). Might it be source of
the some artifacts with pbc ?
so if I unders
Trajectory frames written by mdrun are not post-processed to guess how you
would like PBC to be treated for whatever purpose you have next. So if a
molecule straddles a periodic boundary given the current center position,
that's what it looks like. If there are things you want to do, then there's
t
Dear Gromacs users!
I have performed long md run. From the production trajectory by means of
trjconv -f md_.trr -s cam.tpr -dt 10 -e 300 -sep -o ./pdbs/.pdb # extract
conformers from first 300 ps each 10ps steps
I've extracted 10 conformers in the desired time step
Than when I perform MD on
9 matches
Mail list logo
