Hi poonam,

     I would suggest before running the simulation you can read the paper ( link attached below) and still the drude force field is under development, you can run some sample simulations of that force field.

   You can get the sample simulations in the following link  http://www.ks.uiuc.edu/Research/Drude/

All the Best

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3092300/

Your system has become unstable. Without knowing how you have prepared the system and what the contents of the run input file are, it's hard to say what the solution is. While the force field is still under development, published parameters are stable.

Thanx for your suggestions. Udhaya, I gone through the paper you recommended. Now I am getting error like this:

"ERROR: HardWallDrude> The drude is too far away from atom 84 d = 0.668625!

ERROR: HardWallDrude> The drude is too far away from atom 16 d = 0.572179!

ERROR: HardWallDrude> The drude is too far away from atom 21 d = 1.2668!

ERROR: HardWallDrude> The drude is too far away from atom 26 d = 0.697086!

ERROR: Constraint failure in HardWallDrude(); simulation may become unstable.

ERROR: HardWallDrude> The drude is too far away from atom 16 d = 0.695524!

ERROR: Constraint failure in HardWallDrude(); simulation may become unstable.

ERROR: HardWallDrude> The drude is too far away from atom 74 d = 0.921504!

ERROR: Constraint failure in HardWallDrude(); simulation may become unstable.

ERROR: Constraint failure in HardWallDrude(); simulation may become unstable.

ERROR: Constraint failure in HardWallDrude(); simulation may become unstable.

ERROR: HardWallDrude> The drude is too far away from atom 6 d = 0.732559!

ERROR: Constraint failure in HardWallDrude(); simulation may become unstable.

ERROR: HardWallDrude> The drude is too far away from atom 16 d = 0.702784!

ERROR: Constraint failure in HardWallDrude(); simulation may become unstable.

ERROR: Constraint failure in HardWallDrude(); simulation may become unstable.

ERROR: Exiting prematurely; see error messages above.

====================================================

What should I check for the error.?

You need to tell us how you built the system, what's in it, and provide your full input file.  Either the system was insufficiently minimized or the run settings are causing instability. Without that information, we can only guess.

I used following script for minimization, followed by equilibration step, but also get the same error (like ..."ERROR: HardWallDrude> The drude is too far away from atom 84 d = 0.668625!..) in minimization step:

structure ../step2/step2_drude.xplor.psf

coordinates ../step2/step2_drude.pdb

set temp 300;

set outputname step3_mini;

temperature $temp;

outputName $outputname;

firsttimestep 0;

restartfreq 500;

dcdfreq 1000;

dcdUnitCell yes;

xstFreq 1000;

outputEnergies 125;

outputTiming 1000;

# Force-Field Parameters

paraTypeCharmm on;

exec mkdir -p toppar

exec sed -e "s/^ATOM/!&/g" -e "s/^MASS/!&/g" -e "1,/read para/d" \

-e "s/^BOM/!&/g" -e "s/^WRN/!&/g" ../toppar_drude/toppar_drude_master_protein_2013b.str > toppar/toppar_drude_master_protein_2013b.str

exec sed -e "s/^ATOM/!&/g" -e "s/^MASS/!&/g" -e "1,/read para/d" \

-e "s/^BOM/!&/g" -e "s/^WRN/!&/g" ../toppar_drude/toppar_drude_lipid_2013b.str > toppar/toppar_drude_lipid_2013b.str

exec sed -e "s/^ATOM/!&/g" -e "s/^MASS/!&/g" -e "1,/read para/d" \

-e "s/^BOM/!&/g" -e "s/^WRN/!&/g" ../toppar_drude/toppar_drude_model_2013b.str > toppar/toppar_drude_model_2013b.str

exec sed -e "s/^ATOM/!&/g" -e "s/^MASS/!&/g" -e "1,/read para/d" \

-e "s/^BOM/!&/g" -e "s/^WRN/!&/g" ../toppar_drude/toppar_drude_polyol_2013b.str > toppar/toppar_drude_polyol_2013b.str

exec sed -e "s/^ATOM/!&/g" -e "s/^MASS/!&/g" -e "1,/read para/d" \

-e "s/^BOM/!&/g" -e "s/^WRN/!&/g" ../toppar_drude/toppar_drude_carbohydrate_2013b.str > toppar/toppar_drude_carbohydrate_2013b.str

exec sed -e "s/^ATOM/!&/g" -e "s/^MASS/!&/g" -e "1,/read para/d" \

-e "s/^BOM/!&/g" -e "s/^WRN/!&/g" ../toppar_drude/toppar_drude_nucleic_acid_2013b_no_rna.str > toppar/toppar_drude_nucleic_acid_2013b_no_rna.str

parameters toppar/toppar_drude_master_protein_2013b.str;

parameters toppar/toppar_drude_lipid_2013b.str;

parameters toppar/toppar_drude_model_2013b.str;

parameters toppar/toppar_drude_polyol_2013b.str;

parameters toppar/toppar_drude_carbohydrate_2013b.str;

parameters toppar/toppar_drude_nucleic_acid_2013b_no_rna.str;

# These are specified by CHARMM

exclude scaled1-4

1-4scaling 1.0

switching on

vdwForceSwitching no;

seed 1426164479

mergeCrossterms on

# You have some freedom choosing the cutoff

cutoff 12.0;

switchdist 10.0;

pairlistdist 16.0;

stepspercycle 20;

pairlistsPerCycle 2;

# Integrator Parameters

timestep 0.1;

rigidBonds all;

nonbondedFreq 1;

fullElectFrequency 1;

# Use Drude polarizable model

drude on

drudeTemp 1

drudeHardwall on

drudeDamping 20.0

drudeBondLen 0.2

drudeBondConst 40000

drudeNbtholeCut 5.0

# read system values written by CHARMM (need to convert uppercases to lowercases)

exec tr "\[:upper:\]" "\[:lower:\]" < ../step2/step2_drude.str | sed -e "s/ =//g" > step2_drude.str

source step2_drude.str

# Periodic Boundary conditions. Need this since for a start...

cellBasisVector1 $a 0.0 0.0;

cellBasisVector2 0.0 $b 0.0;

cellBasisVector3 0.0 0.0 $c;

cellOrigin 0.0 0.0 $zcen;

wrapWater on;

wrapAll on;

wrapNearest off;

# PME (for full-system periodic electrostatics)

exec python ../checkfft.py $a $b $c > checkfft.str

source checkfft.str

PME yes;

PMEInterpOrder 6;

PMEGridSizeX $fftx;

PMEGridSizeY $ffty;

PMEGridSizeZ $fftz;

# Pressure and volume control

useGroupPressure yes;

useFlexibleCell no;

langevin on

langevinDamping 1.0

langevinTemp $temp

langevinHydrogen off

# constant pressure

langevinPiston on

langevinPistonTarget 1.01325;

langevinPistonPeriod 50.0;

langevinPistonDecay 25.0;

langevinPistonTemp $temp

colvars on

colvarsConfig step3_mini.col

minimize 20

run 200

# remove harmonic restraints and make restart file

eval colvarbias [concat changeconfig [list bb_rmsd "forceconstant 0"]]

minimize 20

run 200

I'm guessing 20 steps of minimization simply isn't enough here.  I would try a more thorough minimization, a few hundred steps, with atoms restrained and Drudes free to move.  Then turn off all restraints and minimize another few hundred steps.  Don't issue the "run" command, because clearly dynamics is failing at this point.  Inspect the output of minimization carefully and make sure the Drudes haven't strayed too far.  What you're seeing is polarization catastrophe, which is common if the system is not adequately minimized or constructed.  It is common practice to simulate the system for a while with the additive CHARMM36 force field first, as a pre-equilibration, before preparing the system with Drude.  It helps get around some of these issues.