VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Wed Jul 20 2011 - 10:20:35 CDT

Are any of the atom types longer than four characters? The latest CHARMM
forcefields have six-character types, which technically breaks the PSF
format and causes various issues like the one you describe, although NAMD
can still handle it.

-----Original Message-----
From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
Leonardo Trabuco
Sent: Wednesday, July 20, 2011 9:41 AM
To: Edward Lyman
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: autoionize adds too many ions

Hi Ed,

Could you please send me a copy of your system off-list? I'll try to
track down the problem.

Thanks,
Leo

On Fri, Jul 15, 2011 at 9:34 PM, Edward Lyman <edward.lyman_at_gmail.com>
wrote:
> Hi all,
>
> I have built a micelle with 100 or so neutral detergent molecules. I
> have checked the charge on each detergent molecule, it is ~10**-16e. I
> built a water box around it, and then tried to use the autoionize
> plugin to add 0.150 mM NaCl. After adding ions, the plugin complained
> that the system has a non integer charge. For some reason 394 Cl ions
> were added, and 27 Na. Any thoughts on what I'm doing wrong? Been
> banging my head on the wall for a day over it...
>
> Best,
> Ed
>
> ps --- I am using vmd 1.9
>
> 

-- 
Leonardo Trabuco, Postdoctoral fellow (Russell group)
CellNetworks, University of Heidelberg, Germany
http://www.russelllab.org/people/leo/