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: [email protected]
2018-05-08 17:22 GMT+08:00 Alex <[email protected]>:
"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" <[email protected]> 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: [email protected]
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==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
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