Thank you. I have referred to the manual and changed these parts as the
manual told me:
in ffgmx.itp:
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
2 1 no 1.0 1.0
in ffgmxnb.itp:
[ nonbond_params ]
; i j func a b c6
O O 2 92137.86 45.62876437 3090
ZN O 2 51108.27 27.92516056 0
ZN ZN 2 0 0.1 0
But there is no change in the generated .top file.
When I use grompp, the errors are :
ERROR 1 [file ffgmxnb.itp, line 68]:
Trying to add LJ (SR) while the default nonbond type is Buck.ham (SR)
Maybe somewhere else need to be changed. Anyone knows why and how?
Thank you in advance.
----- Original Message -----
From: "Mark Abraham" <mark.abra...@anu.edu.au>
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Sent: Friday, February 20, 2009 6:02 PM
Subject: Re: [gmx-users] combination rules -- the part aboutthe
combinationrules
Shuangxing Dai wrote:
Thanks for your answer. I changed the non-bond parameters in ffgmxnb.itp.
like
; i j func a b c6
Zn O 2 ... ..... .... But error occured..
ERROR 1 [file ffgmxnb.itp, line 270]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
ERROR 2 [file ffgmxnb.itp, line 271]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
ERROR 3 [file ffgmxnb.itp, line 272]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
I think I have indicated that the function type is 2 (means Buckingham).
Anything else need to do with this ?
... specify that the default nonbonded type is not LJ? Have a look in
Chapter 5 of the manual.
Also, I want to fix some atoms in the boundary and specify displacement
to some atoms, anayone knows how to do this?
You can freeze groups of atoms, or use position restraints, or pull groups
of atoms, but you should look first in the manual for the information that
is there.
Mark
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