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Re: [ESPResSo-users] (no subject)]
From: |
Kai Szuttor |
Subject: |
Re: [ESPResSo-users] (no subject)] |
Date: |
Mon, 31 Aug 2015 11:48:36 +0200 |
User-agent: |
Mutt/1.5.21 (2010-09-15) |
Hi,
what are you doing in the warmup section of your simulation?
The usual agenda is:
- cap the forces in your system with "inter forcecap Fmax"
- integrate a few hundred steps
- increase Fmax
- integrate a few hundred steps
- ...
A little snippet:
for { set Fmax 10.0 } { $Fmax < 300.0 } { set Fmax [expr $Fmax*1.125] }
{
inter forcecap $Fmax
imd position
integrate 200
puts "Fmax: $Fmax"
}
Cheers,
Kai
On Mon, Aug 31, 2015 at 02:52:23PM +0530, Nairhita Samanta wrote:
> Hi all!
> I was trying to simulate a polymer with FENE bond conncting the
> monomers. But I am getting this error message
> "Start warmup integration:
> At maximum 30 times 100 steps
> Stop if minimal distance is larger than 0.9
> background_errors { ERROR: bond broken between particles 3 and 2. Distance
> vector:...."
>
> Can anyone tell me where is the problem.
>
> I am also putting here a small part of the code
>
> inter 2 fene 7.0 2.0
>
> append vtf_bonds "polymer"
> polymer 1 $nummon $b_l mode RW bond 2
> set pid 0
> set start_pid $pid
> for {set i 0} { $i < $nummon } {incr i} {
> set posx [expr $b_l*rand()]
> set posy [expr $b_l*rand()]
> set posz [expr $b_l*rand()]
>
> part $pid pos $posx $posy $posz type 1
> incr pid
> }
> set end_pid [expr $pid-1]
> append vtf_bonds "bond " $start_pid "::" $end_pid "\n"
> set start_pid $pid
>
>
> Thanks in advance,
> Nairhita
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