[gmx-users] pure methane condensation in NVT simulation
Alex
nedomacho at gmail.com
Wed May 9 18:53:11 CEST 2018
This 4x4x180 nm periodic NVT box is just incredibly bizarre. I didn't
check your use of walls carefully, maybe this is intended as a capillary
of some sort (I think it is impolite to post grompp's mdouts).
Anyway, not important, because 100 ns is not enough to reach equilibrium
for a system like this, as evidenced by a density gradient obtained in
the final structure, i.e. you likely have a slowly propagating sound
wave after that initial highly ordered placement of your CH4 beads. A
wave like this would be possible regardless of confinement -- merely the
effect of huge anisotropy. I will not be able to continue the results
obtained with that box, maybe others have more time for this kind of
stuff...
Can you use insert-molecules to fill a cubic box (say, 5x5x5) and do a
proper EM + dynamic relaxation run (NPT with Berendsen barostat) for,
say, 20-30 ns?
Alex
On 5/9/2018 6:26 AM, Ming Geng wrote:
> 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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