[gmx-users] gmx 4.5 issue with grompp

[hess at sbc.su.se]

Hi,

Yes, that fix is correct.

I also just committed fixes for pressure coupling with twin-range
interactions (and thus multiple time step integration).

Berk

> 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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>
>
>
> --
> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
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>