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From: Ana Vila Verde
Subject: Re: [ESPResSo] RIGID_BOND
Date: Thu, 17 Jul 2008 16:56:05 +0200
User-agent: Thunderbird (X11/20080501)

Hi Mehmet,

Thanks for the tip about setting the time_step before defining the rigid_bond. That's what I was doing in my own simulations (purely by chance) so that's not the cause of my problems problem.

I implemented a variation of SHAKE that is molecule-specific. It's more efficient than regular SHAKE but the trade-off is that you have to re-code it every time the geometry of your simulated molecule changes. Attached please find the relevant reference. I can send you my Espresso code for my molecule if you'd like to do the same thing for your molecule and you'd like to have an example.

Best regards,


Mehmet Sayar wrote:

One has to set the time_step before defining the rigid_bond, apparently.
If will add a check for this into the code.

Right now, for a two-atom system the algorithm seems to work.


Mehmet Sayar wrote:
Hi All,

I am considering to use the rigid_bond feature, but not much success yet.
I am using
ESPResSo: 2.0.6r, Last Change: June 23rd, 2008

I set up a system with only two particles, which are bonded via a rigid_bond.
{0 pos 2.0 2.0 0.0 type 0 v -0.0 -0.0 -0.0 f 0.0 0.0 0.0} {1 pos 3.0 2.0 0.0 type 0 v -0.0 -0.0 -0.0 f 0.0 0.0 0.0}
{0 RIGID_BOND 1.0 0.001 -0.008}

The output from [inter] command seems a bit confusing, since I gave a tolerance level as:
inter 0 rigid_bond 1. 0.001 0.0001
but the printed tolerance levels differ.

If I issue an "integrate 0" command, I get:
0: VEL CORRECTIONS IN RATTLE failed to converge after 1000 iterations !!

Any suggestions? Is the rigid_bond feature working? Is there anyone actively using it?

Thanks in advance,

Best wishes,


Ana Vila Verde
Post-doctoral scholar
FOM Institute for Atomic and Molecular Physics [AMOLF]
P.O.Box 41883
1009 DB Amsterdam
The Netherlands
Phone: +31-20-6081392
Fax: +31-20-6684106
E-mail: address@hidden

University of Minho
Physics Center
Campus de Gualtar
4710-057 BRAGA

Attachment: bailey2008MILCSHAKE.pdf
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