[gmx-users] RE : long-term drift and crash

David van der Spoel spoel at xray.bmc.uu.se
Thu Aug 23 08:32:18 CEST 2007

Stéphane Téletchéa wrote:
> BON Michael a écrit :
>> Hi,
>> Sorry fot no answering accurately.
>> Here is new insight for understanding my problem.
>> In fact, even simulations of pure water (tip4p and tip4p_ew) don't work !
>> And those simulations crash with a strange periodic pattern : still 
>> using g_msd, I observe
>> on the msd plot sudden jumps that occur exactly every 10.000 ps ! By 
>> "jump" I mean a violent
>> increase of the slope of the curve that lasts a short time, which is 
>> exactly 0.1 ps each time in my case. The curve is linear with the 
>> correct diffusion constant otherwise. I observe such jumps between 
>> 10.0 and 10.1 ps, 20 and 20.1 ps 30 and 30.1 ps, and so on, and each 
>> time the jumps have a higher magnitude than the previous one, till the 
>> simulation crashes.
>> I don't see anything in my parameters that could explain such a 
>> periodicity of 10.000 ps. I tried to half the timestep, and it halved 
>> the duration of the jump, which thus became 0.05, but it didn't 
>> changed the periodicity of 10 ps. Changing tau_t had no consequence.
>> Here are again my parameters for water simulation : constraints = 
>> all-bonds
>> dt = 0.002
> I think you should either use
> - constraints = h-bonds,   dt = 0.002
> or
> - constraints = all-bonds, dt = 0.004
> but not a combination of both.
> Constraining all-bonds is *merely only* for getting a bigger time step 
> for md, but for regular simulations, i would definitely only constrain 
> h-bonds and use dt=0.002.
> Cheers,
> Stéphane
Note that this is a matter of taste (and school of education / 
indoctrination). all-bonds does not allow longer than 2 fs for systems 
containing hydrogens, since the angle vibrations also have a high 
frequency. In practice most simulations with constraints = h-bonds are 
done with dt = 1 fs.

It seems that the original poster has other problems though. Maybe the 
system is freezing. It could also be that your installation is broken in 
some way.

David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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