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: [email protected]
2018-05-08 18:38 GMT+08:00 Justin Lemkul <[email protected]>:
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]
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send
a mail to [email protected].
--
Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/
Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to [email protected].
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
[email protected] | (540) 231-3129
http://www.thelemkullab.com
==================================================
--
Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/Support
/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to [email protected].
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to [email protected].
