[gmx-users] combination rules -- the part aboutthecombinationrules
shuangxingdai at gmail.com
Wed Mar 4 06:54:42 CET 2009
Thank you for your help. I checked all the force field, all of them are with
default non-bond params in LJ. So I still need to try new solution.
I add my non bond parameters in the .top file generated. Force field files
were not changed. Then I use grompp, the error was:
'[ nonbond_params ]'
Invalid order for directive nonbond_params
Rather confused by setting up Buckingham potential parameters...
Thank you very much!
2009/2/26 Berk Hess <gmx3 at hotmail.com>
> But do you need any other parameters than zinc and oxide?
> If not, you can simply remove all other parameters.
> If you need other atoms as well, you will need to find
> a consistent force field, probably or completely LJ
> or completely Buckingham.
> > Date: Thu, 26 Feb 2009 09:22:26 +1100
> > From: Mark.Abraham at anu.edu.au
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] combination rules -- the part
> > Shuangxing Dai wrote:
> > > Yes, "add parameters for crystalline zinc oxide, which require
> > > Buckingham nonbonded interactions", that is what I am doing. I think I
> > > have changed all the necessary parts for the Buckingham potential. Is
> > > there any direct way to accomplish my goal?
> > No, because it's not a reasonable goal. Your new atomtypes are talking a
> > different vdW "language". That doesn't work.
> > > Since in ffgmxnb.itp, all the nonbond_params are LJ if the default type
> > > is 1. I only changed the parameters for Zn and O to Buckingham
> > > parameters. And you said "add your functions in the right form in your
> > > molecule ] section" , I cannot find the right place to change.
> > Chapter 5 of the manual.
> > > And what
> > > force field to choose if not ffgmx?
> > That's your homework I'm afraid. You'll have to read the literature.
> > Mark
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