[gmx-users] constraints hbonds with 4.6

Berk Hess gmx3 at hotmail.com
Mon May 21 14:47:28 CEST 2012


I swapped two arguments to a function call. I have fixed it and it should appear soon
in the public repository. You can find the fix below.



diff --git a/src/kernel/topshake.c b/src/kernel/topshake.c
index c5f3957..78961c5 100644
--- a/src/kernel/topshake.c
+++ b/src/kernel/topshake.c
@@ -204,7 +204,7 @@ void make_shake (t_params plist[],t_atoms *atoms,gpp_atomtype_t at,int nshake)
            p.C1 = pr->param[i].C2;
            add_param_to_list (&(plist[F_CONSTR]),&p);
          } else {
-            copy_bond(pr,i,j++); 
+             copy_bond(pr,j++,i); 
        pr->nr = j;

> Date: Mon, 21 May 2012 11:13:46 +0200
> From: sebastian.waltz at physik.uni-freiburg.de
> To: gmx-users at gromacs.org
> Subject: [gmx-users] constraints hbonds with 4.6
> Hi all together,
> I am testing the 4.6 dev version of gromacs with heterogeneous
> acceleration (force field: amber99-ildn) on a 95 residue protein (all
> atom model) in SPCE and run into major troubles using in the .mdp file
> option constraints = hbonds with the default lincs parameters. The
> system is exploding with the standard lincs warning (relative constraint
> deviation after LINCS ......). Everything is working fine with the
> option constraints = all-bonds or when I constrain all bonds with
> hydrogen atoms manually in the .top file (which is a lot of effort).
> Using gmxdump to search the .tpr file for the constraints I can't find
> the bond constraints using the constraints = hbonds. Therefore I am
> wondering if the very useful option is not included in the 4.6 version
> of grompp or if there is something equal I don't know anything about.
> Thank a lot for any response
> Sebastian
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