etc.
So the trajectory and edr files will be always the same but check-point
files updated (if I will be needed to go back )
Actually it may produce some mismatching between the files...
2018-06-22 16:22 GMT+02:00 Own 12121325 :
> Thanks Mark!
>
>
> assuming that I am interesting to
> standard way of grouping related files, called a directory, and using cd is
> not any more difficult than -deffnm), and you can just use the default file
> naming:
>
> (cd step7; mpirun -np whatever gmx_mpi mdrun -s extended)
>
> Mark
>
> On Fri, Jun 22, 2018 at 11:0
-cpi step7_1.cpt
2018-06-22 10:57 GMT+02:00 Mark Abraham :
> Hi,
>
> The previous checkpoint has the _prev suffix, in case there is a problem
> that might require you to go further back in time.
>
> Mark
>
> On Fri, Jun 22, 2018, 10:46 Own 12121325 wrote:
>
> >
P.S. what the difference between name.cpt and name_prev.cpt produced by
mdrun? What check-point should correspond to the last snapshot in trr file ?
2018-06-22 10:17 GMT+02:00 Own 12121325 :
> In fact there is an alternative trick :-)
> If I rename a tpr file via gmx convert-tpr and th
> On 6/21/18 2:35 AM, Own 12121325 wrote:
>
>> and without append flag it will produce an output in the separate file,
>> won't it?
>>
>
> No, because appending is the default behavior. Specifying -append just
> invokes what mdrun does on its own. If you want a separ
and without append flag it will produce an output in the separate file,
won't it?
gmx convert-tpr -s init.tpr -o next.tpr -extend 50
gmx mdrun -s next.tpr -cpi the_last_chekpoint.cpt
2018-06-21 1:12 GMT+02:00 Justin Lemkul :
>
>
> On 6/19/18 4:45 AM, Own 12121325 wrote:
>
>
the_last_chekpoint.cpt -append
it will produce the second part of the trajectory as the new file
(next.trr) or merge together the first and the second part ?
Thank you!
Gleb
2018-06-18 21:00 GMT+02:00 Justin Lemkul :
>
>
> On 6/18/18 9:11 AM, Own 12121325 wrote:
>
>
Justin Lemkul :
>
>
> On 6/14/18 4:01 AM, Own 12121325 wrote:
>
>> Hello,
>>
>> I wonder to know if it's necessary to provide edr file for the completed
>> part of the simulation in order to continue the md job assuming that I
>> provide the trajectory (wit
Hello,
I wonder to know if it's necessary to provide edr file for the completed
part of the simulation in order to continue the md job assuming that I
provide the trajectory (with coordinates and velocities) using
gmx convert-tpr.
Does the ensembles produced by mdrun will be the same following
Dear GROMACS users,
Using gmx energy I am trying to compute surface tension for the membrane
system in GROMACS under different surface tension. In the model surface
tension was modeled by various negative lateral pressure:
Pxy surf*surftension
1 bar -33.8847
-10 bar 155.696
-20 bar 240.326
-30
Dear Gromacs Users!
I am interesting how is possible to obtain the value for the surface
tension via the output from the gmx energy.
E.g. on the example I have two outputs where in the second case the ST were
introduced via the adding the negative lateral pressure along XY:
# 1) no surface
Dear Gromacs Users,
I have found that 2 ps is a standard value for the tau_t for SD integrator.
Since it is a reverse friction constant, does it means that the values
below 2 ps will provide stronger coupling with thermostat (more virtual
collisions => more viscosity) and the values above 2 ps
?
Or for that case I need to switch to full anisotropic pressure coupling,
introducing a negative pressure along one selected direction ( e.g along x
or y)?
thanks!
2017-09-26 12:37 GMT+02:00 Own 12121325 <own12121...@gmail.com>:
> So the question - what the difference will be betwee
which is the compression
for the membrane along xy.
2017-09-25 17:29 GMT+02:00 Own 12121325 <own12121...@gmail.com>:
> Thanks, Andre!
>
> but I have found a lot of peppers, where people have applied constant
> surface tension simulation using Semi-isotropic coupling. Assuming tha
e-tension
> Andre
>
> On Mon, Sep 25, 2017 at 5:38 AM, Own 12121325 <own12121...@gmail.com>
> wrote:
>
> > Dear Gromacs users!
> >
> > I wonder to ask whether is possible to perform simulations in NPgT
> ensemble
> > with the explicit definition of the surf
Dear Gromacs users!
I wonder to ask whether is possible to perform simulations in NPgT ensemble
with the explicit definition of the surface tension value. My system is
composed of the lipid bilayer solvated in water.
I have found that switching compressibility along x-y to zero and
introducing
Dear Gromacs users!
I wonder to ask regarding mdp setups for the simulation of membrane
bilayers with the introduction of DEFORM (non-equilibrium MD) with the aim
to simulate a shearing of the water.
1 - assuming that I'm doing a simulation using semi-isotropic coupling,
does the switching of
Hello,
with the aim to simulate a shear stress using DEFORM non-equilibrium
option, I need to calibrate the deformations rates of the box (nm ps-1)
against the experimental value characterized for shear stress (10 dyn/cm2 ~
1 pascal).
Therefore, I would like to know what deformations rates set
Hello,
with the aim to simulate a shear stress using DEFORM non-equilibrium
option, I need to calibrate the deformations rates of the box (nm ps-1)
against the experimental value characterized for shear stress (10 dyn/cm2 ~
1 pascal).
Therefore, I would like to know what deformations rates set
Dear Gromacs users!
I would like to use Langevin's thermostat in my simulation of the membrane
protein. I am interesting what values of tau_t will be appropriate for such
simulation, assuming that I would like to create a "soft" equilibration
conditions with slower relaxation times via coupling
Dear GROMACS users,
I would like to perform non-equilibrium simulation adding a shear flow on
the liquid in my bio-membrane system composed of lipids and water. By means
of the applications of the deformations I would like to shear a water in
X-Y dimensions along the surface of the membrane.
21 matches
Mail list logo
