[gmx-users] 回复：Re: interaction potential parameters Between H2O And CO2

[Justin Lemkul]

On 9/13/15 12:55 PM, hzj1000 wrote:
> So how to deal with CO2 ～H2O interaction in GROMACS?
>

To accomplish the stated goal in the original post, one uses [nonbond_params], 
as I said.  Using a *purely* LJ approach to this interaction, is incorrect.  But 
the use of [nonbond_params] to override combination rule values for LJ does not 
preclude the use of electrostatic interactions, as well.  Whether or not this 
ultimately is a valid physical model depends on what is published in this area 
and what you find from your simulations using this model.

-Justin

> 发自我的小米手机
>
> 在 2015年9月14日 上午12:38，"Vitaly V. Chaban" <vvchaban at gmail.com>写道：
>
>     CO2/H2O bonding is irreproducible using LJ only.
>
>
>     On Sun, Sep 13, 2015 at 12:36 PM, Justin Lemkul <jalemkul at vt.edu
>     <mailto:jalemkul at vt.edu>> wrote:
>
>      >
>      >
>      > On 9/13/15 11:26 AM, Zhongjin He wrote:
>      >
>      >> Dera GMX user,
>      >>
>      >>
>      >> I have simulated CO2 in water, using SPC/E for water, EPM2 model for CO2.
>      >> I decide to use Lorentz-Berthelot mixing rule for H2O-H2O and CO2-CO2 LJ
>      >> interaction parameters. But for CO2-H2O LJ interaction paramters,  I do not
>      >> want to use  Lorentz-Berthelot mixing rule, instead, using the more
>      >> accurate LJ  papameters, which are  fitted potential of CO2–H2O  from the
>      >> ab initio calculation results.
>      >>
>      >>
>      >> I do not know how to set up this, could Non-bonded tabulated interactions
>      >> in gromacs be able to set up this kind of interacions between CO2 and H2O?
>      >> Thanks !
>      >>
>      >>
>      > To override combination rule values, use a [nonbond_params] directive with
>      > the pre-computed LJ parameters for each pair for which you wish to use
>      > those values.
>      >
>      > -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
>     <mailto: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

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