Re: [gmx-users] Gromacs versions 4.0.5 and 4.5.4

[Itamar Kass]

Hi Sapna, I had the same problem few weeks ago. Apparently, some parameters are different (eg. nstpcouple). Cheers, Itamar PS I found out that I prefer to stick to 4.0.7.

--- Begin Message --- That seems possible Mark. I had actually assumed that Itamar extracted a .gro from the 4.0.7 simulations and created a new .tpr with 4.5.4 grompp. If that was the case, then I would still be surprised that it had instability problems. One sees a lot of charmm papers where people do slow heating, but my experience with gromacs is that not too many people worry about maintaining the velocities from their NVT simulations for their NPT simulations (or restrained -> unrestrained) and that it works out just fine. On the other hand, I don't see too many gromacs reaction field studies either, so perhaps it all makes sense to those who use these methods.

Thanks again,
Chris.

On 2/09/2011 12:59 AM, chris.neale at utoronto.ca wrote:

That all makes sense Tsjerk.

I wonder if mdrun terminations based on LINCS warnings should come with an additional message to explain that one may try running for a while with nstpcouple=1.

That tip might be a good thing for the wiki page on that.

Also, I'm still a little curious about a question that Itamar asked a few posts ago:

"If this is the case, why 5 ns simulations done with 4.0.7 crashed when extended it using 4.5.4?"

Mark provided a good explanation about how this could be possible, but I've never seen lincs warnings or systems blowing up after 5 ns of equilibration. I fully realize that it may take even us of simulation to properly equilibrate statistical properties, but in my experience it is far outside of ordinary to require >5 ns of equilibration to avoid systems blowing up.

It's hard to say without more detail of how the extension occurred, and
knowing how much ensemble data got lost. It's still conceivable some
horrible mismatch occurred (e.g. virial over-written by some other
data), but not really worth exploring properly. I'd just expect to have
to re-equilibrate upon changing code version, and just not attempt such
an extension.

Mark

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

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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

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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

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--- End Message ---

On 19/10/2011, at 12:08 PM, Sapna Sarupria wrote: Dear All, I have a simulation set up for a mixture of carbon dioxide and water system which runs perfectly on Gromacs 4.0.5 version. I have run these simulations at different temperatures and pressures, from the same starting configuration and the simulation proceeds smoothly in the 4.0.5 version. However, when I use exactly the same files to run the simulation in 4.5.4 version, the system crashes and writes out several pdb files. I was wondering if there is anything specific that has been changed between the two versions. I have pasted the mdp file of the simulations below. Any input will be much appreciated. MDP File  title               =  100% occupancy CO2 hydrate ; a string cpp               =  /lib/cpp                 ; c-preprocessor dt                  =  0.002                    ; time step nsteps          =  15000000                 ; number of steps nstcomm      =  10                       ; reset c.o.m. motion nstxout          =  0000                    ; write coords nstvout          =  0000                    ; write velocities nstlog             =  25000                    ; print to logfile nstenergy       =  500                      ; print energies xtc_grps          =  OW_HW1_HW2_CO2  nstxtcout         =  1000 nstlist               =  10                       ; update pairlist ns_type            =  grid                     ; pairlist method coulombtype    =  PME rvdw                  =  1.2                      ; cut-off for vdw rcoulomb          =  1.2                      ; cut-off for coulomb rlist                    =  1.2                      ; cut-off for coulomb DispCorr          =  EnerPres Tcoupl              =  Nose-Hoover ref_t                  = 270  tc-grps              =  System tau_t                 =  0.5  Pcoupl             =  Parrinello-Rahman Pcoupltype      =  semiisotropic            ; pressure geometry tau_p                =  1.0   1.0                ; p-coupoling time compressibility   =  4.5e-5  4.5e-5           ; compressibility ref_p                     =  30.5  30.5               ; ref pressure gen_vel               =  yes                      ; generate initial vel gen_temp             =  260                      ; initial temperature gen_seed             =  372340                   ; random seed constraint_algorithm = shake constraints         =  all-bonds  ------- Thank you, Sincerely, Sapna -- gmx-users mailing list    gmx-users@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 the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists ----- "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut =========================================== | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu ============================================

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