[gmx-users] pure methane condensation in NVT simulation

[Ming Geng]

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.

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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