Re: [ESPResSo-users] Fwd: Problem with output

[Nairhita Samanta]

This is how I place the polymer

for {set i 0} {$i < $n_poly} {incr i} {
polymer 1 $n_mono $l_poly start [expr ((($fact+1)*$n_janus)+$i*$n_mono)] mode SAW 0.5 5000000 types 3 FENE 0
}

Even if the polymers are not placed randomly initially, after warm up, they should follow sufficiently distinct trajectory in different run.

On Wed, May 4, 2016 at 4:42 PM, Peter Košovan <address@hidden> wrote:

Please provide a minimal working example, otherwise we can only speculate about the possible reasons.

Greetings,

peter

On Wed, May 4, 2016 at 1:11 PM, Rohit Goswami <address@hidden> wrote:

Perhaps the polymer placement loop has no incorporation of the random variable?

Rohit Goswami
B.Tech II
Dept. Of Chemical Engineering
HBTI Kanpur

On Wed, May 04, 2016 at 4:39 PM, Nairhita Samanta <address@hidden> wrote:

Hi Peter!

This problem was not arising when I had a simpler system. However if I have many polymers in a system, this is happening. Although the volume fraction is same from the system with simple particles.

Regards,

Nairhita

On Wed, May 4, 2016 at 4:30 PM, Peter Košovan <address@hidden> wrote:

Yes, there is something you might do:

1. reduce your simulation script to a minimal working example which reproduces the problem

2. attach it to your mailing

If you start with different seeds, you certainly get different trajectories. But there could be other reasons why your script is not doing what you want it to.

Greetings,

peter

On Wed, May 4, 2016 at 12:53 PM, Nairhita Samanta <address@hidden> wrote:

Hi everyone!

I am providing seed to the code in the following way

expr srand ([pid])

But the configurations are still coming to be identical every time. Is there anything else I have to do?

Regards,

Nairhita

On Sun, May 1, 2016 at 11:12 AM, Nairhita Samanta <address@hidden> wrote:

Thank you everyone for your quick response. I will look into this book and the script. If the problem still persists, I will mail again.

Regards,
Nairhita

On Apr 30, 2016 9:22 PM, "Florian Weik" <address@hidden> wrote:

Hi,
if you do not set a seed, Espresso and the random numbers provided by Espresso in TCL (by the t_random command) behave deterministically, which means that if you do not set a different seed, the script will produce the same output. I am not sure how rand, which is provided by TCL behaves.

If you are not sure about PRNGs and their meaning for MD simulations you should look that up in a standard textbook like Frenkel and Smit.

Hope that helps,
Florian

On Apr 30, 2016 3:34 PM, "Nairhita Samanta" <address@hidden> wrote:

Hi all!

       I have this strange problem with my code. Whenever I am running a code, it is giving me the exact same output, i.e. the position and velocity of each particle at each time step coming to be identical from my previous run. I have changed the name of the input and output files, but every time I am seeing the same problem. If you have any solution regarding this problem, please suggest.

Regards,

Nairhita

--

Dr. Peter Košovan

Department of Physical and Macromolecular Chemistry

Faculty of Science, Charles University in Prague, Czech Republic

Katedra fyzikální a makromolekulární chemie

Přírodovědecká fakulta Univerzity Karlovy v Praze

www.natur.cuni.cz/chemistry/fyzchem/
Tel. +420221951290

Fax +420224919752

--

Dr. Peter Košovan

Department of Physical and Macromolecular Chemistry

Faculty of Science, Charles University in Prague, Czech Republic

Katedra fyzikální a makromolekulární chemie

Přírodovědecká fakulta Univerzity Karlovy v Praze

www.natur.cuni.cz/chemistry/fyzchem/
Tel. +420221951290

Fax +420224919752