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Re: Constraint violated by particle

From: David Sean
Subject: Re: Constraint violated by particle
Date: Tue, 12 Nov 2019 10:04:51 -0500

Hi Ahmad,

My guess is that that the particles crossed the pore constraint during
the warmup phase. Try visualizing what happens right before/after the
error to confirm this.

Normally, the LJ interaction you have should not allow the particles
to cross the constraint. However, during the warmup there is an LJ cap
that reduces the repulsion between the particles and the wall. This
opens a short window of opportunity for the crossing that I think
occurs. There are many ways around this issue depending on what you
want, for example:

i) Consider having the flag penetrable=True to stop the simulation
from halting when this occurs (set it to to penetrable=False after
you've finished the warmup)
ii) Init the polymer far from the pore
iii) Init the polymer as a SAW
iv) Tweak the warmup loop (rate at which the cap rises)
v) Add the pore AFTER the polymer warmup


Le mar. 12 nov. 2019 à 09:11, Ahmad Reza Motezakker <address@hidden> a écrit :
> Dear EspressoMD users,
> I am trying to simulate couple of polymer chains with SimplePore constraint. 
> There is LJ interaction between the particles.
> During the warmup process, I face "constraint violated by particle".
> Could you pleas help me to get over this Error?
> A part of my code is attached to this email. Thank you in Advance.
> Best Regards,
> Ahmad Reza

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