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 <jalem...@vt.edu <jalem...@vt.edu>> To: gmx-us...@gromacs.org <gmx-us...@gromacs.org> Subject: Re: [gmx-users] Grompp errors while changing combination rules Message-ID: <d15873b3-233f-0e08-b700-8798a61ee...@vt.edu <d15873b3-233f-0e08-b700-8798a61ee...@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. -Justin* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.