[gmx-users] gmx 4.5 issue with grompp

[Roland Schulz]

Alan,

with the following change your example works for me.

diff --git a/src/gmxlib/inputrec.c b/src/gmxlib/inputrec.c
index 581ae4c..e148612 100644
--- a/src/gmxlib/inputrec.c
+++ b/src/gmxlib/inputrec.c
@@ -169,7 +169,7 @@ int ir_optimal_nstpcouple(const t_inputrec *ir)
 {
     int  nmin,nwanted,n;

-    nmin = pcouple_min_integration_steps(ir->etc);
+    nmin = pcouple_min_integration_steps(ir->epc);

     nwanted = nst_wanted(ir);

Or you can also update from git.

@Berk: Could you please verify that this fix is correct?

Roland

On Sat, Jul 31, 2010 at 2:22 PM, Alan <alanwilter at gmail.com> wrote:

> I am trying this test of mine:
>
>
> wget -c "
> http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=1BVG"
> -O 1BVG.pdb
> grep 'ATOM  ' 1BVG.pdb>| Protein.pdb
>
> pdb2gmx -ff amber99sb -f Protein.pdb -o Protein2.pdb -p Protein.top -water
> spce -ignh
>
> editconf -bt triclinic -f Protein2.pdb -o Protein3.pdb -d 1.0
>
> genbox -cp Protein3.pdb -o Protein_b4ion.pdb -p Protein.top -cs
>
> cat << EOF >| em.mdp
> define                   = -DFLEXIBLE
> integrator               = cg ; steep
> nsteps                   = 200
> constraints              = none
> emtol                    = 1000.0
> nstcgsteep               = 10 ; do a steep every 10 steps of cg
> emstep                   = 0.01 ; used with steep
> nstcomm                  = 1
> coulombtype              = PME
> ns_type                  = grid
> rlist                    = 1.0
> rcoulomb                 = 1.0
> rvdw                     = 1.4
> Tcoupl                   = no
> Pcoupl                   = no
> gen_vel                  = no
> nstxout                  = 0 ; write coords every # step
> optimize_fft             = yes
> EOF
>
> cat << EOF >| md.mdp
> integrator               = md
> nsteps                   = 1000
> dt                       = 0.002
> constraints              = all-bonds
> nstcomm                  = 1
> ns_type                  = grid
> rlist                    = 1.2
> rcoulomb                 = 1.1
> rvdw                     = 1.0
> vdwtype                  = shift
> rvdw-switch              = 0.9
> coulombtype              = PME-Switch
> Tcoupl                   = v-rescale
> tau_t                    = 0.1 0.1
> tc-grps                  = protein non-protein
> ref_t                    = 300 300
> Pcoupl                   = parrinello-rahman
> Pcoupltype               = isotropic
> tau_p                    = 0.5
> compressibility          = 4.5e-5
> ref_p                    = 1.0
> gen_vel                  = yes
> nstxout                  = 2 ; write coords every # step
> lincs-iter               = 2
> DispCorr                 = EnerPres
> optimize_fft             = yes
> EOF
>
> grompp -f em.mdp -c Protein_b4ion.pdb -p Protein.top -o Protein_b4ion.tpr
> \cp Protein.top Protein_ion.top
>
> echo 13 | genion -s Protein_b4ion.tpr -o Protein_b4em.pdb -neutral -conc
> 0.15 -p Protein_ion.top -norandom
>
> \mv Protein_ion.top Protein.top
>
> grompp -f em.mdp -c Protein_b4em.pdb -p Protein.top -o em.tpr
>
> mdrun -v -deffnm em
>
> grompp -f md.mdp -c em.gro -p Protein.top -o md.tpr
>
> And it fails for the command above with:
>
> -------------------------------------------------------
> Program grompp, VERSION 4.5-beta1
> Source code file: inputrec.c, line: 161
>
> Software inconsistency error:
> Unknown epc value
>
>
> Any ideas? Thanks,
>
> Alan
> --
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> >>http://www.bio.cam.ac.uk/~awd28<<
>
> --
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