VMD-L Mailing List

From: Ioana Cozmuta (ioana73_at_gmail.com)
Date: Wed Jun 22 2005 - 20:59:47 CDT

Hi Tom,
 I am trying to use your script at other concentrations but it crashes with
the following error message:
"Assertion failed in file "../../libC/lang_support/throw.cxx", line 1614"
and then with a segmentation fault/core dump.
I was wondering if you tried to use it at 1M or 1.5 M. The only thing I did
is change the value of 0.15 in the script into 1 respectively 1.5.
 I have 37402 water molecules in my input structure. This means that for 1M
the script should add 37402/55.5= 673 ion pairs. However the script only
counts 35593 water molecules for which it will only add 641 ion pairs. I
think this could be solved by redefining the water molecule selection.
In some cases the program will stop at addition 408 (Cl) and 422 (Na), in
others at 612 (Cl) and 561 (Na).
 I would appreciate any suggestion you might have.

Thank you,
Ioana
  
 On 5/19/05, Thomas C. Bishop <bishop_at_tulane.edu> wrote:
>
> Greetings VMD,
>
> Please add this to your script library.
>
> Here's a script I wrote that addes Na+ and Cl- to a system that already
> has
> water. I said in JBSD v22n6 2005 that I'll make it freely available so
> here
> it is.
>
> It does not neutralize the system but merely replaces random waters with
> Na+
> and Cl- so that the effective excess ion concentration is 150mM NaCl.
>
> (if you have a charged system such as DNA you'll still need to add
> neutralizing ions. there's already a tool from ks.uiuc.edu<http://ks.uiuc.edu/>that does this)
>
> Happy VMDing.
> TOm
>
> --
> http://dna.cbr.tulane.edu
>
> Center for Bioenvironmental Research
> Tulane and Xavier Universities
> 1430 Tulane Avenue SL-3
> New Orleans, LA 70112
> Phone: 504-988-6203 Fax: 504-988-6428
> bishop_at_tulane.edu
> -----------------------------------------
> Alternate Contact:
> Center for Computational Sciences
> Voice: (504) 862-8391
> -----------------------------------------
>
>
> 

-- 
Ioana Cozmuta, Ph.D.
Eloret Corporation
NASA Ames Research Center
http://people.nas.nasa.gov/~ioana/
w (650) 604-0993, h (408) 732-1399