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

[David van der Spoel]

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