[gmx-users] Fine tune the RDF of water around a dummy metal

[Justin Lemkul]

On 10/12/16 6:41 PM, Nash, Anthony wrote:
> I've only been able to make contact with a colleague of the original author, and they have been extremely helpful with suggestions but the values still lies out range of that published.
>
> Therefore, I was hoping for some useful suggestion from individuals with more experience than I in the guts of Gromacs on what parameter beyond, charge, sigma, epsilon, mass, FC and eq distances, could contribute to a shift in RDF from metal to oxygen of water.
>

We'll need to see the guts before anyone can comment.  Can you share force field 
files, topology(ies), etc?  And link the paper you're trying to reproduce, to 
make sure we all know exactly what you're trying to do?

-Justin

> Thanks
> Anthony
>
> Dr Anthony Nash
> Department of Chemistry
> University College London
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Justin Lemkul [jalemkul at vt.edu]
> Sent: 12 October 2016 22:56
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Fine tune the RDF of water around a dummy metal
>
> On 10/12/16 5:32 PM, Nash, Anthony wrote:
>> Hi all,
>>
>> I¹m trying to fine tune the rdf of tip3p water molecules around a central
>> metal dummy molecule ("Force Field Independent Metal Parameters Using a
>> Nonbonded Dummy Model²), essentially a central metal (with vdw parameter
>> and -1 charge) covalently bonded to six Œdummy¹ atoms (no vdw parameters,
>> each with a +0.5 charge). Despite all my efforts at recreating the RDF
>> from the published work, my first peak deviates by almost 0.8 Angstroms.
>> The original publication showed that a deviation from their rdf resulted
>> in a large deviation from the correct solvation free energy. Also, a metal
>> demonstrating a deviation of around 0.8 angstrom in a water box will more
>> than likely prevent the metal from settling in plane to the nitrogen atoms
>> of a heme group when the parameters are put into practice.
>>
>> I have looked into adjusting the following in my attempt at bringing the
>> first hydration shell closer to the dummy atom:
>>
>> -adjusting the sigma & epsilon (started from the published values I¹ve
>> iteratively gone through tens of paired values, with sigma never getting
>> below 0.48129. Any attempt at doing so causes steepest descent to crash
>> during an energy minimisation)
>> -shortened the equilibrium bond lengths of the central metal atom to its
>> bonded dummy atoms
>> -increased the positive charge on the dummy atoms whilst reducing the
>> negative charge on the central metal atom
>>
>> 0.32 Angstrom is as close as I can get it without the energy minimisation
>> from crashing out (excessive force).
>>
>> A bit of a long shot but any suggestions on how I could tune these
>> parameters further?
>>
>
> What do the authors say when you tell them you can't reproduce their published
> results?
>
> -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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-- 
==================================================

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

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