From: Salvatore Mario Cosseddu (S.M.Cosseddu_at_warwick.ac.uk)
Date: Thu Oct 27 2011 - 12:20:26 CDT
I'll keep in mind your suggestion. I was very interested in
understanding this behaviour. Many thanks again!!
On 27/10/11 18:12, Chris Harrison wrote:
> A charge nullifying correction is applied to periodic PME simulations,
> conceptually like an inverse charge nullifying field.
> It is however better to balance the charge in your system with solvated
> ions, as the nullification correction is only an approximation.
> Simulating a neutral system is always better.
> No responsible scientist prefers charges perpetuated through the infinite
> axises of the periodic box. Even if a nullifying correction usually
> fixes it. ;)
> Chris Harrison, Ph.D.
> Theoretical and Computational Biophysics Group
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
> char_at_ks.uiuc.edu Voice: 773-570-0329
> http://www.ks.uiuc.edu/~char Fax: 217-244-6078
> Salvatore Mario Cosseddu<S.M.Cosseddu_at_warwick.ac.uk> writes:
>> Date: Thu, 27 Oct 2011 18:00:12 +0100
>> From: Salvatore Mario Cosseddu<S.M.Cosseddu_at_warwick.ac.uk>
>> To: namd-l_at_ks.uiuc.edu
>> Subject: namd-l:PME and net charge in the system
>> User-Agent: Mozilla/5.0 (X11; U; Linux x86_64; en-GB; rv:22.214.171.124)
>> Gecko/20110920 SUSE/3.1.15 Thunderbird/3.1.15
>> Dear all,
>> How NAMD manages a net charge in the system? i.e. A very big system
>> with many charged elements where positive and negative charges are
>> unbalanced, let's say total charge +3 or -4. My idea was that PME do
>> not converge, But it seems that NAMD does not complain. May you tell
>> me if some different approximations are used to handle these events?
>> Salvatore Cosseddu
>> PhD student
>> Centre for Scientific Computing and School of Engineering
>> University of Warwick
>> Coventry CV4 7AL
>> United Kingdom
>> email: S.M.Cosseddu_at_warwick.ac.uk
-- Salvatore Cosseddu PhD student Centre for Scientific Computing and School of Engineering University of Warwick Coventry CV4 7AL United Kingdom email: S.M.Cosseddu_at_warwick.ac.uk
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