[ESPResSo] Fwd: setmd skin

[Mikheil Azatov]

Hi,

Sorry for another email, just wanted to make sure that I understand what gamma in langevin thermostat means. Is it actual friction coefficient or also some kinda reduced unit. I mean is it 3*pi*eta*d for a spherical particle where eta is the viscosity and d is the diameter ?

Thanks, Mike


here is my code
I reduced the code to just severla particles where it's still not working: 
for time_step 0.0128 the particles move very slowly but for 0.0129 they don't...
I calculated all the quantities here in my unit system: they correspond to a particle of diameter 8nm and with a mass of 108 kDa in the water...
The unit of length is nm and the unit of time is 0.1 ns and the unit of energy is kT for 300K

set name  "testfil"
set ident "1"
set vmd_wait  10

setmd box_l 1000 1000 1000
setmd periodic 1 1 1


set n_cross 10
set l_cross 1


for {set i 0} { $i < $n_cross } {incr i} {

  set posx [expr 200*[t_random]+400]
  set posy [expr 200*[t_random]+400]
  set posz [expr 200*[t_random]+400]

  part $i pos $posx $posy $posz type 1 mass 4.32

}



setmd time_step 0.0129; setmd skin 0.5
set temp 1; set gamma 156
thermostat langevin $temp $gamma

    writepsf "$name$ident.psf"
    writepdb "$name$ident.pdb"
    for {set port 10000} { $port < 65000 } { incr port } {
    catch {imd connect $port} res
    if {$res == ""} break
    }
    set HOSTNAME [exec hostname]
    set vmdout_file [open "vmdoutput.script" "w"]
    puts $vmdout_file "mol load psf $name$ident.psf pdb $name$ident.pdb"
    puts $vmdout_file "rotate stop"
    puts $vmdout_file "imd connect 127.0.0.1 $port"
    puts $vmdout_file "mol modstyle 0 0 CPK 5.00000 1.00000 8.000000 6.000000"
    puts $vmdout_file "mol modcolor 0 0 SegName"
   
    close $vmdout_file
    puts "PSF and PDB written. IMD connection on port $port"
    puts "Start VMD in the same directory on the machine you like :"
    puts "vmd -e vmdoutput.script &"
    
    exec /usr/local/vmd/bin/vmd -e vmdoutput.script &
    imd listen $vmd_wait


set integ_steps 5

 
for {set i 0} { $i < 10000 } { incr i} {
 
  puts "t=[setmd time] E=[analyze energy total]"
  
  integrate $integ_steps
  imd positions 

}

set final "final"
writepsf "$name$ident$final.psf"
writepdb "$name$ident$final.pdb"






Mike

---------- Forwarded message ----------
From: Mikheil Azatov <address@hidden>
Date: 2010/6/24
Subject: Re: [ESPResSo] setmd skin
To: "address@hidden" <address@hidden>

Hi,

Thanks for explaining Olaf,

the reason I asked is because in my simulation something weird is happening when I change the time_step. So I have a system of polymers in langevin thermostat. At some time_steps the sytem behaves normally and all the particles experience just thermal motion. When I increase the time_step after some point the system basically explodes. And this transition is very sharp. For example for time-step 0.012 particles move slowly due to thermal motion and for 0.013 the system basically explodes and espresso terminates itself because the particles have such big coordinates. I thought before that it might be because of the skin parameter but after your email and trying different parameters for skin it's obviously not because of it. The reason I change the time step is to make the code run faster. For small time-steps the particles move just very slow and it doesn't make any sense to keep time-step that small.
If anyone had similar problems or has a guess of why could I have them I would really appreciate your response.
Thanks,
Mike

On Thu, Jun 24, 2010 at 3:37 AM, Olaf Lenz <address@hidden> wrote:

Hi!

On 06/23/2010 11:45 PM, Mikheil Azatov wrote:
> Does anyone know what exactly does setmd skin set ? I'm trying to think
> what should it be equal to for my simulation but I cannot figure it out
> what exactly is it. In the manual it says skin for the Verlet list but
> if anyone can say something more I would really appreciate it .

The most important information first: no matter what value for skin you
choose, the *results* of the simulation will always be the same.
However, the speed may change dramatically. Usually, there is an optimal
skin value that minimizes the computation time, which depends on your
system.
Typically, the optimum should be somewhere between 0.1 and 5 times the
maximal interaction range for typical systems. To get the optimum, you
just have to try out.

As for what exactly the skin does, read a description of Verlet lists
for example in Frenkel, Smit "Understanding Molecular Simulations".

Best regards
       Olaf
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