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
--
========================================
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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