[gmx-users] Potential energy
Justin Lemkul
jalemkul at vt.edu
Wed Mar 21 00:18:14 CET 2018
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
==================================================
More information about the gromacs.org_gmx-users
mailing list