[DFTB-Plus-User] NPT simulation

[Puja Goyal]

Hi Ben,

Thanks for the clarification. I have now an ~37 ps NPT simulation trajectory for the water box but the pressure printed in md.out is still around -10^9 Pa. I understand that 37 ps might be very short but I am seeing almost no change in the pressure between the beginning and the end of the simulation. The lattice vector on the other hand has changed from ~15.66 Angstrom to ~15.58 Angstrom. Do you think the simulation is behaving normally? My water box contains 128 molecules and data generation is pretty slow. In case you have experience with NPT simulations on similar systems, can you give me an idea of how long it will take for the pressure to reach the desired value?

Thanks.

Puja.
 
On Oct 11, 2010, at 1:27 PM, Ben Hourahine wrote:

> Hello Puja,
> 
> The difference is that the pressure in the md.out file includes the
> virial pressure term due to the kinetic energy of the atoms, while the
> pressure in the standard output does not. This difference needs to be
> much clearer in the output, or the contributing terms shown separately.
> For your simulation, the values in the md.out file are the correct ones
> to use.
> 
> The md timestep of 1 fs would be quite long if you were not using a
> thermostat, since the O-H bond frequencies are quite high (I use about
> 0.1 fs, but don't often thermostat). You are also using a quite strong
> reselection probability (0.2, so that approximately every 5 MD steps the
> velocities will reset). You probably should test the sensitivity of your
> results to reducing both of these parameters.
> 
> The timescale for the Barostat looks reasonable. As a time, the
> parameter is broadly equivalent to the time it would take for the system
> pressure to change to the target value in the absence of any
> fluctuations. (see Berendsen et al http://dx.doi.org/10.1063/1.448118
> for the details, dimensionally its quite a mess though).
> 
> Regards
> 
> Ben
> 
> Puja Goyal wrote:
>> Hi all,
>> 
>> Has anyone tried doing an NPT simulation with DFTB+? I am doing an NPT simulation on a water box and am unable to figure out why
>> the pressure printed in the md.out file and in the output are different for a given step? I am using the Andersen thermostat with
>> the Berendsen barostat to get an NPT ensemble. The 'driver' section of my input file is as follows:
>> 
>> Driver = VelocityVerlet {
>>  Steps = 50000
>>  TimeStep [Femtosecond] = 1.0
>>  Thermostat = Andersen {
>>    Temperature [Kelvin] = 300.0
>>    ReselectProbability = 0.200000000000000
>>    ReselectIndividually = No
>>    AdaptFillingTemp = Yes
>>  }
>>  Barostat = {
>>    Pressure [Pa] = 101325.0
>>    Timescale [ps] = 0.1
>>  }
>> }
>> 
>> At step 0, the output is:
>> 
>> Pressure:                           0.997522E-04 au     0.293481E+10 Pa
>> 
>> On the other hand, in the md.out file, I have the following for step 0:
>> 
>> Pressure:                           0.854304E-04 au     0.251345E+10 Pa
>> 
>> Could anybody please tell me if my input is OK? Is the timescale value I am using OK (although I am confused by the manual which
>> says the timescale is beta/tau which means that if we neglect the unit of beta, the unit should be time^(-1) )?
>> 
>> I would really appreciate any help.
>> 
>> Puja.
>> 
>> 
>> _______________________________________________
>> DFTB-Plus-User mailing list
>> DFTB-Plus-User at dftb-plus.info
>> http://www.dftb-plus.info/mailman/listinfo/dftb-plus-user
> 
> -- 
>     Dr. B. Hourahine, SUPA, Department of Physics,
>   University of Strathclyde, John Anderson Building,
>          107 Rottenrow, Glasgow G4 0NG, UK.
>    +44 141 548 2325, benjamin.hourahine at strath.ac.uk
>   The University of Strathclyde is a charitable body,
> registered in Scotland, with registration number SC015263
> 
> _______________________________________________
> DFTB-Plus-User mailing list
> DFTB-Plus-User at dftb-plus.info
> http://www.dftb-plus.info/mailman/listinfo/dftb-plus-user