[gmx-users] pure methane condensation in NVT simulation

[耿明]

I tried my simulation with another MD code package using the same potential model and initial configuration. And the result is correct, I get a homogenous gas phase of methane. I have checked my settings in Gromacs several times, But still do not find where could be wrong. Can anyone share me a mdp file to do such a NVT simulation correctly? A simple pure methane box equilibrium in constant Temperature.

Ming Geng

"Justin Lemkul" <jalemkul at vt.edu>写道：
> 
> 
> 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
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