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[ESPResSo] help on dihedral potential
|
From: |
Ana Vila Verde |
|
Subject: |
[ESPResSo] help on dihedral potential |
|
Date: |
Fri, 30 Nov 2007 18:13:16 +0100 |
|
User-agent: |
Thunderbird 1.5.0.12 (X11/20070530) |
Hi all,
I'm trying to simulate a molecule that requires a dihedral potential,
but so far I couldn't make it work. I made a mock molecule (4 beads
making a square) to see what what going on, and I don't get reasonable
results:
1) a simulation where I define a dihedral potential does not produce a
dihedral angle distribution centered around the defined equilibrium
dihedral angle. The probability distribution function of the dihedral
angles looks homogenous between -180 and 180ยบ (similar, but not
identical, to the PDF of the dihedral angles when no dihedral potential
is used). (see *eps or *agr file in attachment)
2) Two different simulations, one where the bending constant is 30 and
another one where it is 300 produce exactly the same results.
I am a new user of Espresso, so it seems likely that I am doing
something wrong in the input file, but I haven't found anything. Could
someone have a quick look at the attached *tcl script to see where I may
have made a mistake?
Thank you all for your help. Best regards,
Ana
--
_______________________________________________________
Ana Vila Verde
Post-doctoral scholar
FOM Institute for Atomic and Molecular Physics [AMOLF]
P.O.Box 41883
1009 DB Amsterdam
The Netherlands
Phone: +31-20-6081392
Fax: +31-20-6684106
E-mail: address@hidden
University of Minho
Physics Center
Campus de Gualtar
4710-057 BRAGA
Portugal
E-mail:address@hidden
_______________________________________________________
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&
set outDir output1
set outName simpleDihedr
#exec mkdir $outDir
set noRunSteps 4000
set outputFreq 20
set n_part 4; set density 0.001
set box_l [expr pow($n_part/$density, 1./3.)]
puts $box_l
setmd box_l $box_l $box_l $box_l
setmd periodic 1 1 1
# defining particles for deoxycholate
set type0 0
set type1 1
set type2 2
puts "making particles"
part 0 pos 0 0 0 type 0
part 1 pos 1 0 0 type 0
part 2 pos 1 1 0 type 0
part 3 pos 0 1 0 type 0
setmd time_step 0.01; setmd skin 0.4
set temp 1; set gamma 1
thermostat langevin $temp $gamma
# defining particle volumes
set lj_eps 1.0
set lj_cutoff 1.12
set ljshift 0.25
set ljoffset 0.0
set lj_sigma 1.0
set lj_sigmah 0.95
#inter 0 0 lennard-jones $lj_eps $lj_sigmah [expr 1.1225*$lj_sigmah] [expr
0.25*$lj_eps] $ljoffset
# defining bonds for deoxycholate
inter 1 fene 30 1.5 ;# these parameters don't allow for bond crossing while
simultaneously allowing for a relatively long time step (see Kremer1989)
part 0 bond 1 1
part 1 bond 1 2
part 2 bond 1 3
#defining dihedrals; dihedrals don't seem to work!!!!
inter 2 dihedral 1 300. 0.
part 1 bond 2 0 2 3
inter 3 angle 30 [expr [PI]/2.]
part 1 bond 3 0 2
part 2 bond 3 1 3
if { [regexp "ROTATION" [code_info]] } {
set deg_free 6
} else { set deg_free 3 }
#equilibration loop
writepsf $outName.psf
writepdb $outName.pdb
set integ_steps 20
puts "equilibrating system: forces are capped"
for {set cap 20} {$cap < 600} {incr cap 20} {
puts "t=[setmd time] E=[analyze energy total]"
inter ljforcecap $cap; integrate $integ_steps
writepdb $outName.pdb -append
}
inter ljforcecap 0
# integration loop
puts "integration loop"
set noCycles [expr $noRunSteps/$outputFreq]
for {set i 0} { $i < $noCycles } { incr i} {
set temp [expr [analyze energy kinetic]/($deg_free/2.0)*$n_part]
puts "t=[setmd time] E=[analyze energy total], T=$temp"
integrate $outputFreq
writepdb $outName.pdb -append
set f [open "./$outDir/config_$i" "w"]
blockfile $f write tclvariable {box_l density}
blockfile $f write variable box_l
blockfile $f write particles {id pos type}
close $f
}
- [ESPResSo] help on dihedral potential,
Ana Vila Verde <=