[gmx-users] Doubt about Free Energy control Minimization

[Varvdekar Bhagyesh Rajendra]

Dear Justin,

It would be helpful if you please explain in a bit more detail about the impact of the settings of table-extension. The manual says "Extension of the non-bonded potential lookup tables beyond the largest cut-off distance", but a better insight from you would be definitely more very useful.

I have a slightest idea that it is useful to save computational time. It that is considered true, it shouldn't affect the results, should it?

I would appreciate if you could explain how increasing table-extension can cause permit distorted structures. 

I performed a short study of the effect on increasing table-extension from 1 nm to 10 nm onwards in increments of 1 nm. The inter and intra molecular energies  increased from 1 nm to 4 nm and then were almost the same and with the minimization without any free energy code. Hence, I suspect that table-extension with 4 nm onwards takes into account all interactions while the free energy change goes on. I would appreciate if you could offer any comment on my deduction. 

I couldn't find any distorted structures while the study though, could you suggest any criteria so as to consider if any structure has evolved into a distorted one?

Is there any other way where I can avoid the said warning other than increasing table-extension and maintaining couple-intramol = no in my minimizing code with the free energy addendum.

Thank you,

Bhagyesh

----- Original Message -----
From: "Varvdekar Bhagyesh Rajendra" <bhagyesh.varvdekar at research.iiit.ac.in>
To: gmx-users at gromacs.org
Sent: Friday, June 30, 2017 2:24:09 AM
Subject: Re: [gmx-users] Doubt about Free Energy control Minimization

Dear Justin,

It would be helpful if you please explain in a bit more detail about the impact of the settings of table-extension. The manual says "Extension of the non-bonded potential lookup tables beyond the largest cut-off distance", but a better insight from you would be definitely more very useful.

I have a slightest idea that it is useful to save computational time. It that is considered true, it shouldn't affect the results, should it?

I would appreciate if you could explain how increasing table-extension can cause permit distorted structures. 

Is there any other way where I can avoid the said warning other than increasing table-extension and maintaining couple-intramol = no in my minimizing code with the free energy addendum.

Thank you,

Bhagyesh

----- Original Message -----
From: "Justin Lemkul" <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Sent: Thursday, June 29, 2017 6:48:25 PM
Subject: Re: [gmx-users] Doubt about Free Energy control Minimization

On 6/29/17 5:11 AM, Varvdekar Bhagyesh Rajendra wrote:
> Dear Justin,
> 
> I am getting the same following warning even after minimizing the system twice using cg integrator. This is only when the free energy stuff is inserted in the energy minimization code.
> 
> " WARNING: Listed nonbonded interaction between particles 2263 and 2298 at distance 3f which is larger than the table limit 3f nm.
> 
> This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions.
> 
> IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. "
> 
> 
> When the system is minimized without free energy code, it shows no warning. Hence, I suppose it is due to the free energy code itself with couple-intramol = no.
> 
> I found the warning disappears when couple-intramol = yes. But this is not I would like to do, since intra molecular interactions need not be scaled/perturbed.
> 
> It's definitely true that the "listed interaction inside a smaller molecule you are decoupling during a free energy calculation".
> 
> When the table-extension is increased to 4 nm with couple-intramol = no, the warning again disappears. Should I go forward with this setting and how will it affect the energy minimization of my system?
> 

Increasing the table-extension means mdrun will permit distorted structures that 
may be totally unreasonable.  It is generally unwise to increase it, and 
especially if you're increasing it that much.

-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

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