From: priyodorshi satpati (psatpati_at_gmail.com)
Date: Tue Dec 22 2009 - 08:43:15 CST
Dear all,
I have a model system : Na(+) and Cl(-) in vacuum. In the MD run I want to
fix Cl(-) and allow the Na(+) to move only along x-direction subject to a
harmonic constraint.
My Namd config file is given below:
#############################
structure setup.psf
coordinates move_na_1.pdb
set outputname move_na_1
firsttimestep 0
paraTypeCharmm on
parameters par_all22_prot.inp
exclude scaled1-4
1-4scaling 1.0
switching on
cutoff 16. ;
switchdist 15. ;
pairlistdist 18. ;
stepspercycle 10 ;
timestep 2.0
nonbondedFreq 1
fullElectFrequency 2
*constraints on
consref move_na_1.pdb
conskfile move_na_1.reg
conskcol B
selectConstraints on
selectConstrX off
selectConstrY on
selectConstrZ on
fixedAtoms on
fixedAtomsFile move_na_1.pdb
fixedAtomsCol B*
binaryoutput no
outputName $outputname
restartfreq 100
dcdfreq 100
xstFreq 100
outputEnergies 100
temperature 0
reassignFreq 100
reassignTemp 25
reassignIncr 25
reassignHold 295
run 50000
################################
But when i analyzed the traj (dcd) file I saw Na(+) is moving in all the
direction (x, y, z). Cl(-) is fixed in place as expected. Please let me know
what should i do.
Regards
Satpati
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:53:38 CST