[gmx-users] Doubt about Free Energy control Minimization

[Justin Lemkul]

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" <jalemkul at vt.edu>
> To: gmx-users at 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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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