[gmx-users] Potential energy

[Alex]

Thanks Justin.

On Tue, Mar 20, 2018 at 3:02 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/20/18 2:40 PM, Alex wrote:
>
>> Dear all,
>>
>> The potential energy of my system after two minimization steps (with and
>> without constrained) is converging well, however, it is still positive
>> around 1000 kj/mol !
>> I think it is not a good sign for my system, but, what could be the reason
>> and how I can overcome the issue? The system generated via "gmx
>> insert-molecules" contains 1000 molecules of "C21H28O4".
>>
>
> Look at the individual values of internal (bonded) terms and nonbonded
> terms. Likely the intermolecular interactions are fairly weak, and the
> potential energy of the system is dominated by internal terms, which are by
> definition positive.
>
I changed the minimization criteria, now I have a negative potential energy
around (-332 kj/mo), and below are the list of different energies: the
bond, angle and LJ/Coulomb-14 are positive. Do you think having a weak
intermolecular interactions is a problem for the system?
Energy                      Average   Err.Est.       RMSD  Tot-Drift
------------------------------------------------------------
-------------------
Bond                        819.286        9.2     27.407   -42.6564
(kJ/mol)
Angle                       1948.89        4.4    9.80344    -23.362
(kJ/mol)
Proper Dih.                 252.261      0.011  0.0262872  0.0474904
(kJ/mol)
LJ-14                       8356.14        1.2     2.4604   -7.05906
(kJ/mol)
Coulomb-14                  5798.87       0.19   0.357136   -1.13575
(kJ/mol)
LJ (SR)                    -9800.04       0.11   0.219992  -0.772991
(kJ/mol)
Disper. corr.              -423.936          0          0          0
(kJ/mol)
Coulomb (SR)               -9722.23       0.15   0.284124   0.915601
(kJ/mol)
Coul. recip.                267.995     0.0039  0.0126721  0.0266248
(kJ/mol)
Potential                  -332.748         15    39.6655   -75.3192
(kJ/mol)
Pres. DC                          0          0          0          0  (bar)


Regards,
Alex

>
> Second question;
>> To calculate the RDF between pair of atoms, let's say A and B, I was
>> wondering if those two atoms should be differentiated in index.ndx file
>> from beginning before invoking the gmx gromps?(similar to energygrps) or
>> one can does the simulation without index.ndx and still possible to
>> calculate the RDF between those two atoms?
>>
>
> There is no need for anything like energygrps. If you want to exclude the
> intramolecular contribution to the RDF (if relevant), you have to increase
> nrexcl in the topology and generate a new .tpr, otherwise everything is
> controlled by index groups.
>
> -Justin
>
> --
> ==================================================
>
> 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.biochem.vt.edu/people/faculty/JustinLemkul.html
>
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