[gmx-users] Grompp errors?

Jones de Andrade johannesrs at gmail.com
Mon Jun 26 22:05:11 CEST 2006

Hi all!.

I was trying to simulate a complex cation in MeCN solution and I got 2
strange warnings to me:

processing topology...
WARNING 1 [file "ff_emi.itp", line 7]:
  Overriding atomtype CT
WARNING 2 [file "ff_emi.itp", line 11]:
  Overriding atomtype H1

But I did found that strange because, as you can see in the file
attached, the entries CT and H1 are just called once.

A second thing that called my attention is the following line that
grompp gives me: "Generating 1-4 interactions: fudge = 0.5". It's not
wrong, since I put this fudge for the VdW interactions, BUT I also
placed a different fudge for the intramolecular coulombic interations
(0.8333), using these lines in the ".top" file I created:

[ defaults ]
; nbfunc      com-rule    gen-pairs      fudgeLJ  fudgeQ
    1            2          yes           0.5000  0.8333

Shouldn't grompp output two fudge parameters instead of only one?

Are those known issues? I just found those warnings in case of use of
standard force fields, what is not the case. The fudge output I could
not find any possible answer.

Thanks a lot for everything in advance.

-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: ff_emi.itp
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060626/f78616af/attachment.ksh>

More information about the gromacs.org_gmx-users mailing list