[gmx-users] Re: fudgeQQ (again ...)

Lianqing Zheng lzheng at me.rochester.edu
Thu Dec 7 21:58:09 CET 2006

Thanks, Chris!

I'm using AMBER FF, so those are the scaling factors in this force
field. Actually I never used standard Gromacs/Gromos ff and always make my
own top file from scratch.


On Thu, 7 Dec 2006 chris.neale at utoronto.ca wrote:

>> Thanks a lot, Janne! I finally got it! Thanks for your inspiration! I
>> added 1-4 pairs in [pairs] and then got the right values. I thought
>> Gromacs would automatically find 1-4 pairs.
>send the structure to pdb2gmx and the value of genpairs will be  
>determined from your ffXXX.itp file. As far as I know, this is only in  
>this way that the [pairs] section will be generated in the output.top  
>file. If your system is not a protein, then you need to add the paris  
>section (and in fact create the entire .top file) by hand.
>By the way, why are you using the combination of genpairs=yes  
>fudgeLJ=0.5 and fudgeQQ=0.8333 ? This is not a valid combination for  
>any force field that comes in the standard gromacs distribution.
>gmx-users mailing list    gmx-users at gromacs.org
>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

More information about the gromacs.org_gmx-users mailing list