Heating problem for protein/ligand complex

From: Alessandro Ruda (alessandro.ruda_at_su.se)
Date: Fri Sep 13 2019 - 13:31:56 CDT

Dear Namd comunity,

I'm running a simulation on a protein/complex system and I'm having problems with the heating step.

The problem is that after the minimization step included in the script, the temperature goes up immediately to the temperature the system is supposed to reach gradually and then stays constant for the rest of the run.

Please see below the script I've been using. Any suggestion would be greatly appreciated!

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structure /xxx.psf
coordinates /xxx.pdb
bincoordinates /xxx.restart.coor

set temperature 293

firsttimestep 0
temperature $temperature

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 14.0
margin 0

# Integrator Parameters
timestep 1.0 ;
rigidBonds water ;
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
wrapWater on
wrapAll on

# Constant Temperature Control
langevin on ;
langevinDamping 1 ;
langevinTemp $temperature
langevinHydrogen off ;

# PBC
cellBasisVector1 57.33 0.0 0.0
cellBasisVector2 0.0 79.77 0.0
cellBasisVector3 0.0 0.0 55.31
cellOrigin 74.51337432861328 1.4879035949707031 0.30966851115226746

# PME
PME yes
PMEGridSpacing 1.0
PMEGridSizeX 58
PMEGridSizeY 80
PMEGridSizeZ 56

# Constant Pressure
useGroupPressure yes ;
useFlexibleCell yes
useConstantArea no

langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.0
langevinPistonDecay 50.0
langevinPistonTemp $temperature

# Output
outputName $outputname

dcdfreq 250
outputEnergies 100
outputtiming 100
binaryoutput yes

reassignFreq 5
reassignTemp 0
reassignIncr 1
reassignHold 293

# Minimization
minimize 10000

run 300000 ;# 300ps

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