On 6/27/17 7:43 AM, Varvdekar Bhagyesh Rajendra wrote:
Dear Justin,
When the system is minimized with full interactions with no free energy code, I
see no warnings and the systems is minimized properly.
However, when the free energy code is added with couple-intramol = no, I
encounter the said warning, but still the system can be minimized ignoring the
warning.
When the free energy code is added with couple-intramol = yes, there's no
warning, but the system is again well minimized.
You may need several rounds of energy minimization to get a stable result. Your
final minimization and equilibration should be done under the
conditions/settings that make the most sense for you to model.
-Justin
I would like to learn if its reasonable to ignore the warning in the case where
couple-intramol = no, since I am dealing with a peptide and intramolecular
interactions can suppress the intermolecular interactions.
I intend to perform normal-mode calculations on the resulting intermediates
which are divergent from the Binding energy simulations requiring convergence.
Hence, I presume there shouldn't be much complication in this case. I
understand the approach seems quite outlandish, but still I aspire to execute
the same. Any opinions and/or suggestions in this procedure will be greatly
helpful.
Many thanks,
Bhagyesh.
----- Original Message -----
From: "Justin Lemkul" <jalem...@vt.edu>
To: gmx-us...@gromacs.org
Sent: Tuesday, June 27, 2017 6:42:33 PM
Subject: Re: [gmx-users] Doubt about Free Energy control Minimization
On 6/26/17 9:09 AM, Varvdekar Bhagyesh Rajendra wrote:
Dear Justin,
I have encountered the following warning when I used the following code to
minimize my protein-ligand system when the interaction potential energy between
the protein and the ligand are multiplied by 0.9, 0.8, 0.7,..., 0.2, 0.1.
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/Files/em_steep.mdp
Warning: 1-4 interaction between 2263 and 2298 at distance 1.004 which is
larger than the 1-4 table size 1.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
I suppose this error is due to setting couple-intramol = no. When it is set to
yes, the warning vanishes.
But, this is my desired setting since, I do not intend to scale the intra molecular
interactions even though the ligand is a peptide. Is it reasonable to ignore the warning.
If not , how can it affect my resulting structure ? And are all such interaction
"ignored for the rest of the simulation" ?
So the system is unstable. Try minimizing with full interactions before doing
anything funny with scaling. And I repeat my caution to you that trying to do
an alchemical transformation of a peptide is a very unwise choice. You'll never
get the simulations to converge in a practical amount of time.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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