[CP2K:10607] Re: Equilibration in NVT MD run

Lucas Lodeiro eluni... at gmail.com
Tue Aug 7 01:53:57 CEST 2018


I am not an expert in that, but i can suggest you some things:
The timestep is not the ideal for X-H bonds, less for gas phase molecules,
since the oscillation frecuency is bigger. I would put 0.5 fs.
Other important thing is, the temperature is not well defined for one step
(is a statistical property), less if the sistem just have 50 atoms, maybe
that do not allow a "fast or regular" convergence of temperature.
Also, you are not using a PBC system, i do not know if the kinetic energy, and
therefore the temperature, is well defined.

In my case, I usually use a liquid system (300 atoms) and PBC conditions,
with the same nose-hoover parameters, except for TIMECON=50, but I use a
clasical Molecular Dinamics first the ab-initio MD to obtain a better
guess, with a better correspondence between the kinetic energy and the
potential energy (positions); those systems reached the reference
temperature and equilibrium in less than 1 ps (with the tipical oscilation
around the reference temperature, but well matched the average value). I
feel for the temperature plot, and the initial molecular geometry, you use
an optimiced/relax potential energy geometry, and that can make it longer
time to reached the reference temperature, because the thermasthat must
inject a great amount of kinetic energy to reach the equilibrium.

Sorry if it is not helpful. Regards

2018-08-06 3:39 GMT-04:00 raghav saxena <raghavs... at gmail.com>:

> Hey Martin,
>
>                 I removed the TEMP_TOL=100 line and changed the time
> constant to 20 and I got this but the mean temperature is still not 310
> even after 3.4 ps. Any suggestions?
>
> Regards
> Raghav
>
> On Sun, Aug 5, 2018 at 2:30 AM, M. Brehm <brehmin... at gmail.com>
> wrote:
>
>> Dear Raghav,
>>
>> I could imagine that this effect is due to the "TEMP_TOL   100" line.
>> Please try to comment out this line.
>>
>> Apart from that, a thermostat time constant of 100 fs is relatively weak
>> for an early equilibration. If there is much change in the structure of the
>> system, the coupling of the thermostat might simply be too weak. I
>> recommend to use a lower value (e.g. "TIMECON 20") in the early
>> equilibration stages. The value of 100 fs is fine for production runs or
>> late equilibration.
>>
>> One more comment: Your time step of 1.0 fs is fairly large for a system
>> which contains hydrogen atoms. This is always a matter of taste, but I
>> would go for 0.5 fs if hydrogens are involved. Otherwise, the integration
>> error might become significant, leading to a drifting conserved quantity.
>>
>> Best regards,
>> Martin
>>
>>
>> Am Samstag, 4. August 2018 20:13:51 UTC+2 schrieb Raghav:
>>>
>>> Dear cp2k users,
>>>
>>>                         I am trying to equilibrate my system. I am doing
>>> NVT simulation but the mean temperature of my system is not reaching the
>>> target Temperature (310K) as can be seen in the figure attached. I am using
>>> Nose Hoover Thermostat, Is there some problem with the parameters of the
>>> thermostat or something else is the problem.
>>>
>>> Input file is attached.
>>>
>>> Regards
>>> Raghav
>>>
>>
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