[gmx-users] pure methane condensation in NVT simulation

[Justin Lemkul]

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
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jalemkul at vt.edu | (540) 231-3129
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