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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