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

chris.neale at utoronto.ca chris.neale at utoronto.ca
Thu Sep 1 14:41:58 CEST 2011

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.


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.


> 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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