[gmx-users] Conbination rule

[leafyoung81-group at yahoo.com]

Hi, Zhang

I don't think that's a printing error. 5.1 and 5.2 is for the definition of two parameters given in the whatever [atomtypes] [nonbonded_params] and [pairtypes]. 
5.3 and 5.4 determines how inter-atomic LJ parameters are defined from the two parameters in [atomtypes].

You may find two forcefields and determines sigma and epsilon for same type of atom according to their comb-rule. Every forcefield shall conserve this.
Second, you may derive the parameters for two atoms from [atomtypes] and compare with its given value in [nonbond_params] (e.g. ffgmx2.itp). They may be different but could be the same.

Yang Ye


----- Forwarded Message ----
From: leafyoung81-group at yahoo.com
To: Junfang.Zhang at csiro.au
Sent: Friday, January 06, 2006 10:18:51 AM
Subject: Re: [gmx-users] Conbination rule

Hi, Zhang

I don't think that's a printing error. 5.1 and 5.2 is for the definition of two parameters given in the whatever [atomtypes] [nonbonded_params] and [pairtypes]. 
5.3 and 5.4 determines how inter-atomic LJ parameters are defined from the two parameters in [atomtypes].

You may find two forcefields and determines sigma and epsilon for same type of atom according to their comb-rule. Every forcefield shall conserve this.
Second, you may derive the parameters for two atoms from [atomtypes] and compare with its given value in [nonbond_params] (e.g. ffgmx2.itp). They may be different but could be the same.

Yang Ye

----- Original Message ----
From: Junfang.Zhang at csiro.au
To: leafyoung81-group at yahoo.com; gmx-users-bounces at gromacs.org
Sent: Friday, January 06, 2006 9:37:19 AM
Subject: RE: [gmx-users] Conbination rule

Dear Yang Ye,

It is confusing to understand the explanation of combination rule at the
bottom of page 90 and the top of page 91 of manual-3.2.pdf:

(5.1) for combination 1
(5.2) for combination 2 and 3
(5.3) for combination 1 and 3
(5.4) for combination 2

I am wondering if it is a printing error.

Thanks,

Junfang 


 

-----Original Message-----
From: leafyoung81-group at yahoo.com [mailto:leafyoung81-group at yahoo.com] 
Sent: Thursday, 5 January 2006 4:15 PM
To: Zhang, Junfang (DPR, Clayton)
Subject: Re: [gmx-users] Dummy particle

That is for ratio if you look at the definitions of dummies. I guess, by
the time when the developers wrote the manual, they were short of
symbols for that but left it as empty brackets. =)

For second, I think you are right. But it is 3D, if I am critical, such
conclusion will depend on your projection.

Yang Ye

----- Original Message ----
From: Junfang.Zhang at csiro.au
To: gmx-users at gromacs.org; leafyoung81-group at yahoo.com
Sent: Thursday, January 05, 2006 12:33:47 PM
Subject: RE: [gmx-users] Dummy particle

Dear Yang Ye,

Thank you very much. Your help is deeply appreciated.

When I read Table 5.4 on page 99 of manual-3.2.pdf, there is one line:

(type     directive  #at    func  parameters)
Dummy3fd   dummies3   4     2    a(), d(nm) 

It is clear that d is in unit nm, how about a? What does () mean?

I am not clear about the coordinate reference frame for Figure 4.16
(page 78). For 3fd, if parameter d>0, does it mean that the dummy
particle is on the right-hand side of particle i (as all the
constructing particles are not labeled, I just guess from the context)?

Regards and thanks,

Junfang

 


-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of
leafyoung81-group at yahoo.com
Sent: Wednesday, 4 January 2006 4:07 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Table.xvg

Hi, Zhang
 
It is hard to figure out what you mean exactly. TIP4P is a water model,
not a water-water interaction type (though it implies it). If you would
like to specify different table for different interactions between
groups, you may use, what I have mentioned early, energygrp_table.
 
E.g.
energygrp_table     =  Centers Centers Centers Tails Tails Tails
 
Three groups so I used three types of interaction and supply three files
table_Centers_Centers.xvg
table_Centers_Tails.xvg
table_Tails_Tails.xvg
 
Yang Ye

----- Original Message ----
From: Junfang.Zhang at csiro.au
To: gmx-users at gromacs.org
Sent: Wednesday, January 04, 2006 12:05:06 PM
Subject: RE: [gmx-users] Table.xvg


Dear Gromacs users,


Could you possibly let me know how to
Generate different user defined potential table (table.xvg) for
different interactions? For example, if I choose TIP4p for water and
water interactions, but other user defined function for water-methane?


Thanks,

Junfang
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