[gmx-users] pure methane condensation in NVT simulation

[Ming Geng]

Thanks very much, Justin and Alex.
I am not familiar with Gromacs, I think it should start with some simple
system. I want to do is just a long box(4*4*180nm) of 20032 methane
molecule (density = 0.1853g/cm^3 ).  Fix the temperature at 400K, and then
I can calculate the pressure of the system. I checked with the equation of
state, at 400K, the pressure of this methane should be around 431 bar.
 All the settings files ( Initial structure, mpd file, forcefield files)
can be found in  my github repository
<https://github.com/gengmingchina/MethaneTest_Gromacs/tree/master/Settings>
 (https://github.com/gengmingchina/MethaneTest_Gromacs/tree/master/Settings).
You two or anyone else who would like to do us a favor to check what we
have done wrong in our simulation is welcomed to download the files.
Because we have a run with 100 ns. And we take four snaps from our run. The
pdb files of snaps can be found in the Structure-Snaps folder
<https://github.com/gengmingchina/MethaneTest_Gromacs/tree/master/Structure-Snaps>
 (
https://github.com/gengmingchina/MethaneTest_Gromacs/tree/master/Structure-Snaps
).

Ming Geng




-------------------------------------------------------------
*Dr. Ming Geng（耿明）*
Institute of Geology and Geophysics, CAS

Tel: +86-10-8299-8300
Email: gengming at mail.iggcas.ac.cn

2018-05-08 18:38 GMT+08:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 5/8/18 6:34 AM, Ming Geng wrote:
>
>> Thanks Alex,
>>      "common NVT" I mean is the simulation is only using the T coupling
>> and
>> no P coupling. The T P coupling part was set as following
>>
>> *    ;; TEMPERATURE COUPLING*
>> *     ; Temperature coupling methods *
>> *     Tcoupl                   = nose-hoover*
>> *     ; frequency for coupling temperature*
>> *     nsttcouple               = -1*
>> *     ; Groups to couple separately*
>> *     tc-grps                  = SYSTEM*
>> *     ; Time constant (ps)*
>> *     tau_t                    =  2*
>> *     ; reference temperature (k)*
>> *      ref_t                    = 400      *
>> *   ;; PRESSURE COUPLING     *
>> *   ; pressure coupling methods*
>> *   pcoupl                   = no  *
>> *   ; way of pressure coupling *
>> *   pcoupltype               = isotropic*
>> *   ; frequency for coupling pressure*
>> *   nstpcouple               = -1*
>> *   ; Time constant (ps)*
>> *   tau_p                    = 2*
>> *   ; compressibility in bar^(-1)*
>> *   compressibility          = 4.5e-5 *
>> *   ; reference pressure*
>> *   ref_p                    = 1*
>>
>>       The settings of the whole simulation are simple, but we get a weird
>> result. That is why I am writing here to get help. In our simulation, the
>> only unusual thing is the box size(4x4x180nm). In our test with normal
>> box,
>> like 4 x 4x 4 nm, the result will be correct as we think. Do you think
>> this
>> could be the reason we get a strange result? Thanks a lot.
>>
>
> Your observations likely indicate that the nonbonded model is inadequate.
>
> -Justin
>
>
> Ming Geng
>>
>> -------------------------------------------------------------
>> *Dr. Ming Geng（耿明）*
>> Institute of Geology and Geophysics, CAS
>>
>> Tel: +86-10-8299-8300
>> Email: gengming at mail.iggcas.ac.cn
>>
>> 2018-05-08 17:22 GMT+08:00 Alex <nedomacho at gmail.com>:
>>
>> "Common NVT" and not properly set up NPT for organic fluid simulations?
>>> What could possibly go wrong...
>>>
>>> Alex
>>>
>>>
>>> On May 8, 2018 3:15 AM, "Ming Geng" <gengming at mail.iggcas.ac.cn> wrote:
>>>
>>> Dear all,
>>>        We are trying some MD simulations with Gromacs recently. And we
>>> found
>>> some weird phenomenon in our test. We have about 20k pure methane in a
>>> long
>>> box(4 x 4 x 180 nm). We use OPLS-UA for methane molecule. After a 70ns of
>>> common NVT simulation, we found the methane begin to condensate. The
>>> simulation box shows like
>>>          [methane|    vacuum    |       methane     |    vacuum
>>>  |methane]
>>> .
>>> But at the temperature we simulate, the methane should be in gas phase.
>>>
>>>       Does anyone have any clue how this happens?
>>>
>>>
>>>
>>>
>>> Thanks
>>>
>>>
>>> Ming Geng
>>> -------------------------------------------------------------
>>> *Dr. Ming Geng（耿明）*
>>> Institute of Geology and Geophysics, CAS
>>>
>>> Tel: +86-10-8299-8300
>>> Email: gengming at mail.iggcas.ac.cn
>>>
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>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
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