[gmx-users] Potential energy

[Justin Lemkul]

On 3/20/18 7:15 PM, Alex wrote:
> 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)

I don't see any problems here.

-Justin

>
> 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
>>
>> ==================================================
>>
>> --
>> 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.biochem.vt.edu/people/faculty/JustinLemkul.html

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