[gmx-users] Very large Max Force [Energy minimisation] in water with ions

[Erik Marklund]

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.

Kind regards,
Erik

On 7 Nov 2014, at 05:36, Kester Wong <Kester2014 at ibs.re.kr<mailto:Kester2014 at ibs.re.kr>> 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 <erik.marklund at chem.ox.ac.uk<mailto:erik.marklund at chem.ox.ac.uk>>
받는사람 : "<gmx-users at gromacs.org<mailto:gmx-users at gromacs.org>>" <gmx-users at gromacs.org<mailto:gmx-users at gromacs.org>>
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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