Modar Tutorial
Example 4: Villin headpiece simulation
     step3_add_ions.inp

 

# add counter ions

#

# author: mengen

#

# usage: ./modar step3_add_ions.inp anion=POT cation=CLA ionc=0.1 method=hybrid

#        anion default is  K+

#        cation default is CL-

#        concentration default is 0.1 mol/ml

#

 

#load force field

include "loadff.inc"

 

#anion and cation name

if(! -var anton) anion="POT"

if(! -var cation) cation="CLA"

if(! -var method) {

  method="hybrid"

  echo -hs "no adding ions method specified"

  echo -hs "the default method hydrid will be used"

  echo -hs "or please make a choice bellow"

  echo -hs "  1  MC"

  echo -hs "  2  best size"

  echo -hs "  3  hybrid"

  echo -hsn "  which one:"

  ichoice=gettext()

  if($ichoice==1) method="mc"

  if($ichoice==2) method="bs"

}

echo -hs " using method: $method"

 

#concentration of ions, default value is 0.1 mol/ml

if(! -var ionc) {

  ionc=0.10

  echo -hs "|  no ionc (ion concentration) specified, "

  echo -hs "   default value 0.1 mol/ml will be used"

  echo -hsn "   or tell the concentration here:"

  newionc=gettext()

  if($newionc>0.001) ionc=$newionc

}

echo -hs "|  ion concentration is $ionc mol/ml"

 

if($ionc>100 || $ionc<0) {

  echo -hs "|  ** invalid ion concentration $ionc mol/ml"

}

 

#show arguments

echo -hs "|  anion is $anion"

echo -hs "|  cation is $cation"

 

#load solute

loadmsf file="step1_solute.msf"

 

#load PBC crystal setup

include "pbc.inc"

 

tell msf_info

 

#calc ions accessible volume

tell boxsize

tell volume gridsize=0.5 rprobe=1.4 select="all"

accvol=$boxvol-$molvol

 

#compute number of ions to be added

nion=$ionc*6.021*0.0001*$accvol

npos= int($nion-$netcharge+0.5)

if($npos<0) npos=0

nneg=$npos+$netcharge

 

#show number of ions to add

echo -hs "|  number of $anion need to add: $npos"

echo -hs "|  number of $cation need to add: $nneg"

 

#buildionacc gridsize=2.0 ion=CLA outpdbfile=iongrids.pdb

 

#nonbond setup

nonbond type=pme nblcutoff=12.0 nbcutoff=10.0 swcutoff=8.0 eps=80.0 \

        beta=0.34 ftx=$fftx fty=$ffty ftz=$fftz bsorder=6

 

#build mdcore

build mdcore timestep=0.002 nstep=100 nprint=1 \

     trjfile="test.dcd" frqtrj=100 trjfmt=charmm \

     rstfile="test.rst" frqrst=100 \

     randseed=314159 randtype=old \

     frqresort=20000

 

nnadd=0

npadd=0

 

#init system random seed for MC move try

randseed iseed=20000 sys=true

 

echo -hs "|  adding ions ..."

echo -hs "|  it may take a few minitues, please wait a while"

 

nptot=$npos

nntot=$nneg

 

#adding ions

if($method=="hybrid" || $method=="hy") goto hybrid

else if($method=="bs") goto bestsite

 

:mconly

echo -hs "|  adding ions using MC method"

while($npos>0 || $nneg>0) {

  baddneg=1

  if($npos>$nneg) baddneg=0

  else if($npos<$nneg) baddneg=1

  else {

    #calc the voltage for all accessible grids to determin to add positive or negative first

    addion testonly=true ion=$cation gridsize=1.0

    if(abs($vmin)>$vmax) baddneg=0

  }

 

  if($baddneg==1) {

    nnadd=$nnadd+1

    echo -hs "|    adding a $cation, $nnadd/$nntot"

    addion method=MC ion=$cation nMCtry=100 gridsize=1.0

    nneg=$nneg-1

  }

  else {

    npadd=$npadd+1

    echo -hs "|    adding a $anion, $npadd/$nptot"

    addion method=MC ion=$anion  nMCtry=100 gridsize=1.0

    npos=$npos-1

  }

}

goto doneaddions

 

:bestsite

echo -hs "|  adding ions using best site method"

while($npos>0 || $nneg>0) {

  baddneg=1

  addion testonly=true ion=$cation gridsize=1.0

  echo -hs "|       vmin,vmax,vavg,vsig: $vmin, $vmax, $vavg,$vsig"

  if($npos>$nneg) baddneg=0

  else if($npos<$nneg) baddneg=1

  else{

    #calc the voltage for all accessible grids to determin to add positive or negative first

    if(abs($vmin)>$vmax) baddneg=0

  }

 

  if($baddneg==1) {

    nnadd=$nnadd+1

    echo -hs "|    adding a $cation, $nnadd/$nntot"

    addion method=bs ion=$cation nMCtry=100 gridsize=1.0

    nneg=$nneg-1

  }

  else{

    npadd=$npadd+1

    echo -hs "|    adding a $anion, $npadd/$nptot"

    addion method=bs ion=$anion  nMCtry=100 gridsize=1.0

    npos=$npos-1

  }

}

goto doneaddions

 

:hybrid

echo -hs "|  adding ions using hybrid method"

while($npos>0 || $nneg>0){

  baddneg=1

 

  addion testonly=true ion=$cation gridsize=1.0

  echo -hs "|       vmin,vmax,vavg,vsig: $vmin, $vmax, $vavg,$vsig"

  method=mc

 

  if($npos>$nneg) baddneg=0

  else if($npos<$nneg) baddneg=1

  else {

    #calc the voltage for all accessible grids to determin to add positive or negative first

    if(abs($vmin)>$vmax) baddneg=0

  }

 

  if($baddneg==1) {

     if($vmax-$vavg>0.017) method=bs

  }

  else{

     if($vavg-$vmin>0.017) method=bs

  }

 

 

  if($baddneg==1) {

    nnadd=$nnadd+1

    echo -hs "|    adding a $cation, $nnadd/$nntot  using $method method"

    addion method=$method ion=$cation nMCtry=100 gridsize=1.0

    nneg=$nneg-1

  }

  else{

    npadd=$npadd+1

    echo -hs "|    adding a $anion, $npadd/$nptot  using $method method"

    addion method=$method ion=$anion  nMCtry=100 gridsize=1.0

    npos=$npos-1

  }

}

 

:doneaddions

 

#save solute with ions

savemsf file="step3_with_ions.msf"

savepdb fmt=pdb file="step3_with_ions.pdb"

 

echo -hs "|  output files:"

echo -hs "|    step3_with_ions.msf"

echo -hs "|    step3_with_ions.pdb"

echo -hs "| "

echo -hs "|  it's ready to go next step to put all stuff together:"

echo -hs "|    ./modar -nobak step4_merge_all.inp"

 


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