[gmx-users] pure methane condensation in NVT simulation

[Justin Lemkul]

On 5/8/18 10:11 AM, 耿明 wrote:
> 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.

Please start by sharing what it is that you're actually doing. The 
snippet you provided before is not a full .mdp file.

Have you checked that you get equivalent energies and forces of the 
system in both GROMACS and your other software package? It is important 
to do an apples-to-apples comparison with a single-point energy evaluation.

-Justin

> 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
>>>>
>>>> --
>>>> 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 gmx-users-request at gromacs.org.
>>>> --
>>>> 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 gmx-users-request at gromacs.org.
>> -- 
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (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 gmx-users-request at gromacs.org.

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================