[gmx-users] Temperature control in fix gcmc with fix rigid/nvt/small

[Youzhi Hao]

Sincere apologies to this unrelated post to the mailing system.

Please just ignore it!

 

In fact, when I decided to post a problem that troubles me recently, I
opened then mail client and by coincidence I was just clicking on the
gromacs mailing list which do me a regular push service and thus I switched
to the gromacs recipient by carelessness. I wasn't aware of this until
noticed by Alex, sorry!

Whatever, it's my first thread posted to the gromacs mailing system! 

 

regards,

Youzhi

 

 

On 6/19/2017 12:49 AM, Alex wrote:

It may come as a huge surprise, but this is a mailing list for a 

different software package. ;)

 

 

On 6/19/2017 12:49 AM, Youzhi Hao wrote:

> hi,

> 

> I'm trying to do gcmc simulation of rigid CH4 molecules adsorption
isotherms

> in clay minerals

> 

> by using fix gcmc with fix rigid/nvt/small.

> 

> The coulomb potential was calculated by PPPM.

> 

> The fix rigid/nvt/small was combined with fix_modify dynamic/dof yes

> 

> and fix_modify temp as the LAMMPS Manuals says.

> 

>   

> 

> However, as the simulation going on (after a long time), the CH4 molecules

> were just kept adding to the system,

> 

> leading the pressure far higher than the pressure specified in fix gcmc

> command.

> 

> Also, the system temperature continues increasing up, higher than the

> specified temperature.

> 

> The fix rigid/nvt/small command seems did not thermostat well.

> 

> So, what's the reason lying beneath this unusual phenomenon?

> 

>   

> 

> Part of my input file is :

> 

> variable temp  equal  363.15

> 

> variable press  equal  100.00

> 

> variable fug_coeff equal 0.934

> 

> molecule  ch4  mol.ch4.txt  #full atom methane molecule

> 

> compute Temp_methane methane temp/com

> 

> compute_modify Temp_methane dynamic/dof yes

> 

> fix  mrsnvt  methane  rigid/nvt/small  molecule  temp ${temp} ${temp}
100.0

> mol ch4

> 

> fix_modify  mrsnvt  dynamic/dof  yes

> 

> fix_modify  mrsnvt  temp  Temp_methane

> 

> fix  1  methane  gcmc  1000  1000 500 0 2949499 ${temp} -0.28 0.5 mol ch4
&

> 

> 

>        maxangle 180 rigid mrsnvt pressure ${press}  fugacity_coeff ${

> fug_coeff } full_energy

> 

> run 5000000

> 

>   

> 

> Best regards.

> 

> Youzhi Hao

>