[gmx-users] free energy blank dgdl

[Da-Wei Li]

hi

It seems that your couple-moltype is missing, that is, no molecules will be
turned off interaction.


dawei

On Thu, Feb 17, 2011 at 8:26 AM, Moeed <lecielll at googlemail.com> wrote:

> Hello Justin
>
> Thanks for your attention. Just to remind you: I am getting blank dgdl and
> I found this in log file:
>
> > There are 0 atoms and 0 charges for free energy perturbation
>
>
> ====================================
> EM
> >
> > grompp -f em-l0.mdp -c *.gro -p PE60-0c-itp.top -o em-l0.tpr >&
> > output.grompp_em
> >
> > mdrun -s em-l0.tpr -o em-l0.trr -c em-l0.gro -g  em-l0.log -e em-l0.edr
> > -v >& output.mdrun_em
> >
> > MD
> >
> > grompp -f md-l0.mdp -c em-l0.gro -p PE60-0c-itp.top -o md-l0.tpr -n
> > PE-HEX.ndx>& output.grompp_md
> >
> > mdrun -s md-l0.tpr -o md-l0.trr -c md-l0.gro -g md-l0.log -e md-l0.edr
> > -x md-l0.xtc -dgdl md-l0.dgdl -v >& output.mdrun_md
> ================================
> with mdp :
>
>
> pbc              =  xyz
> energygrps          =  PE HEX
>
> ;        Run control
> integrator          =  md
> dt                  =  0.002
> nsteps              =  500000 ;5000
> nstcomm             =  100
>
> ;        Output control
> nstenergy           =  100
> nstxout             =  100
> nstvout             =  0
> nstfout             =  0
> nstlog              =  1000
> nstxtcout          =  1000
>
> ;        Neighbor searching
> nstlist             =  10
> ns_type             =  grid
>
> ;        Electrostatics/VdW
> ;;;;coulombtype         =  PME
> vdw-type            =  Shift
> rcoulomb-switch     =  0
> rvdw-switch         =  0.9 ;0
>
> ;        Cut-offs
> rlist               =  1.1
> rcoulomb            =  1.1 ;1.0
> rvdw                =  1.0
>
> ;        Temperature coupling
> Tcoupl              =  v-rescale
> tc-grps             =  System
> tau_t               =  0.1     ;0.1
> ref_t               =  400     ;300
>
>
> ;        Velocity generation
> gen_vel             =  yes
> gen_temp            =  300.0
> gen_seed            =  173529
>
> ;        Bonds
> constraints             = all-bonds
> constraint-algorithm = lincs
>
> ;         Free energy control stuff
> free_energy          =   yes
> init_lambda          =   0
> delta_lambda         =   0
> sc_alpha             =   0.5
> sc-power             =   1
> sc_sigma             =   0.3
> couple-lambda0       =   vdw
> couple-lambda1       =   none
> couple-intramol      =   no
>
> ***************************************
> Thank you in advance.
> Moeed
>
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