Chris.
-- original message --
Hi Chris,
I can imagine that the pressure scaling has a more profound effect on
the 'visible' surroundings if a cut-off is used, while this will not
be the case when using PME. So the shock for an atom when the
coordinates are adjusted can be expected to be greater with cut-off
based methods, rendering such simulations less stable. As for SD,
probably that causes sufficient damping of jitter introduced due to
pressure coupling for it not to propagate and cause problems.
But those are just my two cents (about 2.8 dollar cents with current
rates :p).
Cheers,
Tsjerk
On Thu, Sep 1, 2011 at 2:41 PM, <chris.neale at utoronto.ca> wrote:
I am glad that the pressure coupling intervals have been identified as a
source of instability for poorly equilibrated systems as I was
unaware of
that. Still, the fact that the SD integrator also solves the problem
also
suggests that this is simply a poorly equilibrated system. I am not
sure why
PME would run fine and reaction field would give lincs warnings, but
then
again I have no experience with using a reaction field.
Chris.
On 1/09/2011 6:32 PM, Itamar Kass wrote:
Hi Tsjerk,
Thanks for the help, it actually worked. When nstpcouple is set to
1m the
system can be equilibrated (NPT) without LINCS error. I hadn't
thought about
it as I never use NVT (unless doing FE calculations).
Equilibrating with NVT before NPT can be wise when the system starts far
from equilibrium.
Is this mean the 4.5.4 is more sensitive the 4.0.7? Is this effect the
data collected till now? If this is the case, why 5 ns simulations
done with
4.0.7 crashed when extended it using 4.5.4?
IIRC 4.0.x and 4.5.x have different mechanisms for deciding how often to
do global communication for things like T and P coupling. Mostly you can
get away with the same kind of approximation one uses with twin-range
neighbour lists, periodic neighbour list updates, RESPA, etc. where
slowly-varying quantities don't have to be recalculated every step.
However during equilibration (and that includes the transition from
4.0.x to 4.5.x) those assumptions need not be valid. So tuning the
update frequency to be high during transitions is a good idea. Then
relax them and see how you go.
Mark
Also, is this mean I can do my productive run using 4.5.4 with the
default
value of nstpcouple, it seems that setting it to 1 greatly increases
the
computational time. To the best of my knowledge, in prior version
nstpcouple
was set to 1 by default.
Cheers,
Itamar
On 01/09/2011, at 4:47 PM, Tsjerk Wassenaar wrote:
Hi Itamar,
I haven't really followed the discussion and I'm a bit too lazy to
look it all up now ;) But have you tried setting the nst parameters to
1 (except for output). Especially nstpcouple. Note that nstpcouple=1
requires nstlist=1 and nstcalcenergy=1. If that solves the problem,
you may need to extend your equilibration a bit, first relaxing NVT,
followed by NPT with nstpcouple=1, thereafter equilibrating using
productions conditions. It it solves it, maybe the option should be
renamed nstptrouble :p
Hope it helps,
Tsjerk
--
gmx-users mailing list gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use thewww
interface
or send it to gmx-users-request aGROMACS 4.5.4 keep crashing all the
time
Tsjerk Wassenaar tsjerkw at gmail.com
Thu Sep 1 15:48:40 CEST 2011
* Previous message: [gmx-users] GROMACS 4.5.4 keep crashing all
the time
* Next message: [gmx-users] Non-zero total charge
* Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
Hi Chris,
I can imagine that the pressure scaling has a more profound effect on
the 'visible' surroundings if a cut-off is used, while this will not
be the case when using PME. So the shock for an atom when the
coordinates are adjusted can be expected to be greater with cut-off
based methods, rendering such simulations less stable. As for SD,
probably that causes sufficient damping of jitter introduced due to
pressure coupling for it not to propagate and cause problems.
But those are just my two cents (about 2.8 dollar cents with current
rates :p).
Cheers,
Tsjerk
On Thu, Sep 1, 2011 at 2:41 PM, <chris.neale at utoronto.ca> wrote:
I am glad that the pressure coupling intervals have been identified as a
source of instability for poorly equilibrated systems as I was
unaware of
that. Still, the fact that the SD integrator also solves the problem
also
suggests that this is simply a poorly equilibrated system. I am not
sure why
PME would run fine and reaction field would give lincs warnings, but
then
again I have no experience with using a reaction field.
Chris.
On 1/09/2011 6:32 PM, Itamar Kass wrote:
Hi Tsjerk,
Thanks for the help, it actually worked. When nstpcouple is set to
1m the
system can be equilibrated (NPT) without LINCS error. I hadn't
thought about
it as I never use NVT (unless doing FE calculations).
Equilibrating with NVT before NPT can be wise when the system starts far
from equilibrium.
Is this mean the 4.5.4 is more sensitive the 4.0.7? Is this effect the
data collected till now? If this is the case, why 5 ns simulations
done with
4.0.7 crashed when extended it using 4.5.4?
IIRC 4.0.x and 4.5.x have different mechanisms for deciding how often to
do global communication for things like T and P coupling. Mostly you can
get away with the same kind of approximation one uses with twin-range
neighbour lists, periodic neighbour list updates, RESPA, etc. where
slowly-varying quantities don't have to be recalculated every step.
However during equilibration (and that includes the transition from
4.0.x to 4.5.x) those assumptions need not be valid. So tuning the
update frequency to be high during transitions is a good idea. Then
relax them and see how you go.
Mark
Also, is this mean I can do my productive run using 4.5.4 with the
default
value of nstpcouple, it seems that setting it to 1 greatly increases
the
computational time. To the best of my knowledge, in prior version
nstpcouple
was set to 1 by default.
Cheers,
Itamar
On 01/09/2011, at 4:47 PM, Tsjerk Wassenaar wrote:
Hi Itamar,
I haven't really followed the discussion and I'm a bit too lazy to
look it all up now ;) But have you tried setting the nst parameters to
1 (except for output). Especially nstpcouple. Note that nstpcouple=1
requires nstlist=1 and nstcalcenergy=1. If that solves the problem,
you may need to extend your equilibration a bit, first relaxing NVT,
followed by NPT with nstpcouple=1, thereafter equilibrating using
productions conditions. It it solves it, maybe the option should be
renamed nstptrouble :p
Hope it helps,
Tsjerk
--
gmx-users mailing list gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use thewww
interface
or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
