[gmx-users] GROMACS 4.5.4 keep crashing all the time

[chris.neale at utoronto.ca]

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
>>>>
>>
>>
>>
>> -- 
>> 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
>
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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
>>>>
>>
>>
>>
>> -- 
>> 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
>>
>
>
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