On 11/10/14 7:58 AM, Kester Wong wrote:
Dear Justin,
Thank you for the feedback. I have also tried the following:
i) separating OH- and Na+ ions
ii) placing the ions much closer to water droplet
iii) increase the spacing between each ions, i.e. using a larger box
Perhaps I should try having the ions in a larger box, then fill the box with
water molecules and then redo the energy minimisation and NVT?
Well, like Erik said, there really isn't a smoking gun and what I'm observing
might be either causative or symptomatic, there's just no way to know at this
point. I don't know what good any of those three options will do, because I
don't understand what you're trying to accomplish. What was the logic of
putting a lattice of OH- and random Na+ in vacuo above a water droplet? What is
the goal of your simulations?
-Justin
Regards,
Kester
On 11/10/14 5:04 AM, Erik Marklund wrote:
> Dear Kester,
>
> Hm. No obvious smoking gun as far as I can see. You could try a two-step
minimisation where you first do one minimisation with soft-core potentials and
then one without.
>
What's strange to me is the lattice of OH- at the top of the box and the
sodium
ions that are floating out in the middle of nowhere. I don't understand the
construction of this system, but having highly charged stuff in close
contact
and floating around in vacuum certainly looks like it could be trouble.
-Justin
> Kind regards,
> Erik
>
> On 7 Nov 2014, at 05:36, Kester Wong> wrote:
>
>
> Dear Erik,
>
> The starting structure consists of water on graphene that has already
been energy minimised, and subsequently equilibrated (NVT) for 20ns.
> Using that (water droplet on graphene), I added the ions for energy
minimisation.
> I followed a two-step minimisation:
> i) Minimisation with no constraints (-DFLEXIBLE)
> ii) Minimisation with constraints (SETTLES for TIPS3P water, and
(-DCONSTRAINTS) for hydroxide)
>
> With the ions:
> I have tried placing the ions box lower toward water droplet, but the Max
Force remains large upon energy minimisation.
>
> The input files can be accessed here:
>
https://drive.google.com/folderview?id=0B7ym8d6G9-e2dG5pOFQ4SWVyZG8&usp=sharing
>
> The hydroxide parameter is taken from Gerrit Groenhof, based on the
supplementary material in this paper:
> http://dx.doi.org/10.1016/j.bpj.2014.04.062
>
> In short, this model was developed very similarly to the polarisable
version of hydroxide in the SWM4-NDP force field.
> As for sodium and graphene, the topology parameters were taken from
CHARMM27; TIPS3P was used for the water model.
>
> Visualisation after the energy minimisation showed a distorted virtual
site of the hydroxide ions, where one of the four virtual sites no longer conform
to the constraint. So, I am guessing whether the extremely large Max Force
originates from the force constants in the hydroxide topology?
>
> Thank you for your time and assistance!
> -Kester
> --------- 원본 메일 ---------
> 보낸사람 : Erik Marklund>
> 받는사람 : ">">
> 받은날짜 : 2014년 11월 6일(목) 20:35:59
> 제목 : Re: [gmx-users] Very large Max Force [Energy minimisation] in water
with ions
>
> Dear Kester,
>
> The potential energy is highly positive in the first case and the force
is enormous in the second case, so no wonder that they blow up. How did you
prepare these systems?
>
> Kind regards,
> Erik
>
> Erik Marklund, PhD
> Postdoctoral Research Fellow, Fulford JRF
>
> Department of Chemistry
> Physical & Theoretical Chemistry Laboratory
> University of Oxford
> South Parks Road
> Oxford
> OX1 3QZ
>
> On 6 Nov 2014, at 04:31, Kester Wong > wrote:
>
>
> Dear all,
>
> I have been trying to energy minimise ~1980 water (tips3p) molecules with
20 OH- anions (with virtual sites and dummy atoms) and 20 Na+ cations, however, I
always ended up getting a very large Max Force.
>
> Using emtol = 1000 and emstep = 0.0001, I get:
>
> Potential Energy = 3.79607808453231e+09
> Maximum force = 9.86741557582003e+02 on atom 42394
> Norm of force = 2.38846729392462e+01
>
> Using emtol = 700 and emstep = 0.0001, I get:
>
> Potential Energy = -6.43566327273198e+13
> Maximum force = 9.24568347101016e+25 on atom 42262
> Norm of force = 5.74744822148669e+23
>
> As expected, both structures blew up during NVT equilibration.
>
> Could this be due to the arrangement of the ions? I tried separating the
anions and cations in two boxes (placed on top of the water droplet), but that
also yield a very large Max Force.
>
> FYI, the water droplet on graphene was equilibrated for 20ns.
> Any input is greatly appreciated. Thanks.
>
> - Kester
>
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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
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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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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