[gmx-users] combination rules -- the part aboutthe combinationrules

[Berk Hess]

Hi,

Is line 68 one of the lines you have added, or another one?

Berk

> From: shuangxingdai at gmail.com
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] combination rules -- the part	aboutthe	combinationrules
> Date: Sun, 22 Feb 2009 14:55:21 -0700
> 
> 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.Abraham at anu.edu.au>
> To: "Discussion list for GROMACS users" <gmx-users at 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
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the list. Use the www 
> > interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php 
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

_________________________________________________________________
What can you do with the new Windows Live? Find out
http://www.microsoft.com/windows/windowslive/default.aspx
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090222/04fc211b/attachment.html>