[gmx-users] free energy blank dgdl

[Justin A. Lemkul]

Moeed 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                    

By not setting a proper "coulombtype," grompp defaults to "cutoff," which is a 
very inaccurate method.

> 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

You didn't set "couple-moltype" so mdrun doesn't know which molecule to decouple.

-Justin

> 
> ***************************************
> Thank you in advance.
> Moeed
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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