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

Mark Abraham Mark.Abraham at anu.edu.au
Thu Sep 1 10:57:05 CEST 2011

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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