
From:  Owen Hickey 
Subject:  Re: [ESPResSousers] error: constraint violated by particle.... 
Date:  Wed, 19 Feb 2014 15:10:39 +0100 
Hi Dear Axel,I have a system which is concluding a cylinder constraint. I assume a ring in the middle of the constraint and 36 polyelectrolytes are attached to this circular ring, but the error: constraint violated by particle.... always occurs.When I use the PSAW for polyelectrolytes it gets better but still random errors take place.Could you please help me to solve this problem?here is my part of my code:# interaction parameters
set bjerrum 3.0
set accuracy 0.001
set particle_sigma 1.0
set particle_epsilon 1.0
set particle_cutoff 1.12246
set particle_shift 0.25
set constraint_sigma 1.0
set constraint_epsilon 1.0
set constraint_cutoff 0.858374
set constraint_shift 0
set bond_K 7.0
set bond_rcut 2.0#constraintset r 20
set c [expr $box_length/2]
constraint cylinder center $c $c $c axis 0 0 1 radius $r length $box_length direction 1 type 4 penetrable 0
# SET UP THE INTERACTIONS
# bond between the monomers
inter 0 fene $bond_K $bond_rcut
# interaction between the particles
set max_part_type 3
for {set i 0} { $i <= $max_part_type } {incr i} {
for {set j $i} { $j <= $max_part_type } {incr j} {
inter $i $j lennardjones $particle_epsilon $particle_sigma $particle_cutoff $particle_shift 0
}
}
# interaction between the constraint and the particles
for {set i 0} { $i <= $max_part_type } {incr i} {
inter $i 4 ljgen $constraint_epsilon $constraint_sigma $constraint_cutoff $constraint_shift 0 9 3 0.133333 1.0
}
#############################################################
# SET UP THE POLYELECTROLYTES
set z $c
set mypi 3.141592653589793
set j 0
while {$j< 360} {
set x [expr $c+(($r0.001)*sin(($mypi*$j)/180))]
set y [expr $c+(($r0.001)*cos(($mypi*$j)/180))]
set first [expr $num_monomers_per_polymer*(($j/10))]
polymer 1 $num_monomers_per_polymer 1.0 start $first pos $x $y $z mode PSAW charge 1.0 distance 1 types 0 0 FENE 0 constraints
part $first q 0 fix 1 1 1
incr j 10
}# WARMUP INTEGRATION
set min_dist 0.8
set act_min_dist [analyze mindist]
set cap 10
inter forcecap $cap
for {set i 0} { $act_min_dist < $min_dist } {incr i} {
integrate 10000
set act_min_dist [analyze mindist]
incr cap 10
inter forcecap $cap
}
# turn off capping
inter forcecap 0The errors occur when it starts to warm up?In one of last posts you said that we should not cap the potential with walls? why? how can we do it?Thank you,Roya
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