[gmx-users] Re Grompp errors while changing combination rules

Apramita Chand apramita.chand at gmail.com
Wed Jul 18 08:18:37 CEST 2018

Dear Justin,
I have tried the same commands with gromacs version 5.1.2 and the same
errors arise.
You have suggested that the format of what has been provided to grompp may
be wrong. What I did was modify ffnonbonded.itp by leaving the C6, C12
columns empty alongside pair interactions under the [nonbonded params] and
[pairs] headings. (Since I have specified sigma,epsilon values in the
[atomtypes] section(intending to use combination rule 3), the interaction
parameters have to be calculated using these values.)  For example:

*[ nonbond_params ]; i    j func          c6           c12      OM
O  1      OA        O  1      OA       OM  1      OE        O  1
OE       OM  1      OE       OA  1*

*.... etc. *

*and [ pairtypes ]; i    j func             OM        O      OA        O
1      OA       OM  1      OE        O  1      OE       OM  1      OE
OA  1      OW        O  1*
 Then I used this modified ffnonbonded.itp in the topology file like this :

*; Include forcefield parameters#define _FF_GROMOS96#define _FF_GROMOS53A6[
defaults ]; nbfunc    comb-rule    gen-pairs    fudgeLJ    fudgeQQ  1
          3                 yes             1.0           1.0#include
"ffnonbonded_modified.itp"#include "ffbonded.itp"*
I assumed leaving the columns blank will prompt grompp to generate the
interactions and indeed there was a line stating "Generated 1653 of the
1653 non-bonded parameter combinations / Generated 1-4
interactions/Generated 1653 of 1653 1-4 parameter combinations"

What should be the correct method of changing the ffnonbonded.itp or
specifying in the topology file? Please advise.
Thanking you,

Yours sincerely,
Apramita Chand

*Message: 4 Date: Tue, 17 Jul 2018 08:14:50 -0400 From: Justin Lemkul
<jalemkul at vt.edu <jalemkul at vt.edu>> To: gmx-users at gromacs.org
<gmx-users at gromacs.org> Subject: Re: [gmx-users] Grompp errors while
changing combination         rules Message-ID:
<d15873b3-233f-0e08-b700-8798a61ee01e at vt.edu
<d15873b3-233f-0e08-b700-8798a61ee01e at vt.edu>> Content-Type: text/plain;
charset=utf-8; format=flowed On 7/17/18 5:40 AM, Apramita Chand wrote: >
Dear All, > I had enquired earlier about the steps for changing combination
rules in > GROMOS ff. As I understood from your answers, if I am to take
combination > rule 3, I can put  sigma and epsilon for my atomtypes under
the C6 and C12 > columns in ffnonbonded.itp  and these numbers will be
interpreted as sigma > and epsilon when I specify the combination number.
Also, I don't need to > add anything in the non-bonded params section as
the interactions will be > automatically calculated. I have specified the
'gen-pairs'=yes in the The gen-pairs keyword has no real relation to the
combination rule, it's there to do what it says: generate 1-4 pair
parameters when not present in ffnonbonded.itp. > defaults section for this
purpose. But when I try to minimise the system I > get the message: > > Too
many warnings (2862), g_grompp terminated. > If you are sure all warnings
are harmless, use the -maxwarn option. > > > WARNING 2862 [file
ffnonbonded_modified.itp, line 2927]: >    Too few parameters on line
(source file >    /builddir/build/BUILD/gromacs-*

*4.5.7/src/kernel/toppush.c, line 820) Any reason you are using wildly
outdated (and unsupported) software? > > > I had taken the exact same
system and files with combination rule 1 and the > simulation ran smoothly.
> > What could be the problem? Is there anything I have missed out ?Should
I > use the maxwarn option? Absolutely not. "Too few parameters on line"
means the format of what you have provided grompp is not correct. Your
model physics will not be realistic, if the resulting simulation even runs.

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