VMD-L Mailing List

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Tue Jul 09 2013 - 14:25:25 CDT

As Alex mentioned at the end of the refrenced thread. 4.9xxxxxxxe^-6 is
effectively zero.

On 9 July 2013 20:40, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> Hi,
> The discussion of the old version was just to ensure that the
> user tried and repeated the issue with the new version before we
> invested time chasing any bug that may have already been fixed.
>
> From your email below, it's not clear if you're getting an error message
> or not. Are you getting an error message or not? Please show us the
> exact command you ran and the output it gave you.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Sat, Jun 29, 2013 at 06:23:03PM +0530, Revthi Sanker wrote:
> > Dear all,
> > With reference to the thread in the vmd mail list about the
> auto-ionize
> > program:
> > http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/16117.html
> >
> > the reply given was that the error was due to usage of an older
> version
> > of auto-ionize, but I am using vmd version 1.9.1 still my system has
> net
> > charge of 4.9xxxxxxxe^-6 even after the neutralization. I do not know
> if
> > that is the reason why my system is not converging to minima. And how
> do I
> > make the system charge to be zero? I am a beginner to performing
> > simulations and to vmd. kindly provide your valuable suggestions in
> this
> > issue.
> > thank you in advance.
> >
> > Revathi.S
> > M.S. Research Scholar
> > Indian Institute Of Technology, Madras
> > India
> > _________________________________
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>