[gmx-users] Dummy particle

[Junfang.Zhang at csiro.au]

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
_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.