Re: [ESPResSo-users] error: constraint violated by particle....

[Owen Hickey]

Hey Roya,

You might try adding "reflecting 1" to your constraints during the warmup. This should explicitly prevent particles from violating the constraints by applying a  bounce back with the constraint. After the warmup you should be able to delete the constraints and rebuild them without this flag.

Hope that helps,

Owen

On Wed, Feb 19, 2014 at 3:04 PM, roya moghaddasi <address@hidden> wrote:

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

#constraint

set 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 lennard-jones $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 lj-gen $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 $c+(($r-0.001)*sin(($mypi*$j)/180))]
set y [expr $c+(($r-0.001)*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 0

The 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