[gmx-users] Has anyone seen this error befor?

Berk Hess gmx3 at hotmail.com
Wed Sep 15 17:28:19 CEST 2010


Someone forgot to edit topsort.c when added a new dihedral type.
I fixed it for 4.5.2.
The fix is an addition of one line, see below.


diff --git a/src/gmxlib/topsort.c b/src/gmxlib/topsort.c
index fbf7aa4..128e57f 100644
--- a/src/gmxlib/topsort.c
+++ b/src/gmxlib/topsort.c
@@ -61,6 +61,7 @@ static gmx_bool ip_pert(int ftype,const t_iparams *ip)
     case F_ANGLES:
     case F_G96ANGLES:
     case F_IDIHS:
+    case F_PIDIHS:
         bPert = (ip->harmonic.rA  != ip->harmonic.rB ||
                  ip->harmonic.krA != ip->harmonic.krB);

Date: Wed, 15 Sep 2010 08:07:23 -0700
From: mustardt at onid.orst.edu
To: gmx-users at gromacs.org
Subject: [gmx-users] Has anyone seen this error befor?


    Message body

    I started a small 2 nucleic acid system for FEP testing. As well as turning on fep, I set RNA_Chain_A as the couple-moltype. I also set couple-lambda0 and couple-lambda1 to vdw-q and none respectively. I then began a "steep" mdrun and got this error:



    Program mdrun, VERSION 4.5

     Source code file: topsort.c, line: 112


     Fatal error:

     Function type Improper Dih. not implemented in ip_pert

     For more information and tips for troubleshooting, please check the GROMACS

     website at http://www.gromacs.org/Documentation/Errors


    I have searched for this on google and found nothing. Do I need an Improper Dihedral section in my top/itp file? I have ran this same system with fep off and it runs perfectly.


    Any help is much appreciated.



    TJ Mustard

    Email: mustardt at onid.orst.edu

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