Reg autioionize plugin

From: Vidhya Sankar (vidhyasankar7928_at_yahoo.com)
Date: Sat Jul 28 2018 - 01:19:09 CDT

Thank you João Ribeiro sir,
                   I am doing equilibration dynamics (protein/Membrane system) for protein kept above Membrane while protein is kept fixed during my equilibration .     i ran dynamics without adding ions  but later on i needed to add ions  then wish to run my equilibration  dynamics i have used the following force field parameter  and other parameter in my .conf files   
 
paraTypeCharmm      on
parameters          /home/others/ponkvel/namdsvs/dwe/par_all36_lipid.prm
parameters         /home/others/ponkvel/namdsvs/dwe/par_all36_lipid.prm
 parameters          /home/others/ponkvel/namdsvs/dwe/par_all36_prot.prm
 parameters         /home/others/ponkvel/namdsvs/dwe/toppar_water_ions_namd1.str
parameters          /home/others/ponkvel/namdsvs/dwe/par_all36_carb.prm
    parameters         /home/others/ponkvel/namdsvs/dwe/par_all36_cgenff.prm

wrapWater           on
wrapAll             on

# Force-Field Parameters
exclude             scaled1-4
1-4scaling          1.0
cutoff              25
switching           on
switchdist          10.
pairlistdist        25

 constraints on
   consexp 2
  constraintScaling 1
 consref  /home/others/ponkvel/namdsvs/newtutmem2.pdb
 conskfile  /home/others/ponkvel/namdsvs/proteinconstrainedM.cnst
 conskcol B
 margin 3
#  selectConstraints  on
 # selectConstrZ  on
fixedAtoms on
fixedAtomsForces off
fixedAtomsFile  /home/others/ponkvel/namdsvs/proteinconstrainedM.cnst
fixedAtomsCol B
 tclforces on
 set waterCheckFreq              100
 set lipidCheckFreq              100
 set allatompdb                   /home/others/ponkvel/namdsvs/newtutmem2.pdb
 tclForcesScript                 /home/others/ponkvel/namdsvs/keep_water_out.tcl
# eFieldOn yes
# eField 0 0 -0.155

#############################################################
## EXECUTION SCRIPT                                        ##
#############################################################

# Minimization
if {1} {
minimize            100000
reinitvels          100
}

run 2500000 ;# 0.5 ns
                           

with high regards and respect
S.Vidhyasankar

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