VMD-L Mailing List

From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Sat Jul 27 2013 - 15:27:25 CDT

I've faced the same problem in the past. Since it's only VMD (and not NAMD) that does not yet properly handle long atom types, there's a simple solution if all you want to do is neutralize: straight after solvation, run a brief simulation and and search for the line containing "CHARGE" in the log file. Once you've got that, kill the simulation (you do NOT want to keep the trajectory of a non-neutralized system!) and calculate manually the number of ions needed to neutralize (and reach your desired concentration if you wish).

Tristan Croll
Lecturer
Faculty of Science and Technology
Institute of Health and Biomedical Engineering
Queensland University of Technology
60 Musk Ave
Kelvin Grove QLD 4059 Australia
+61 7 3138 6443

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On 27/07/2013, at 2:17 AM, "Revthi Sanker" <revthi.sanker1990_at_gmail.com<mailto:revthi.sanker1990_at_gmail.com>> wrote:

Dear all,
I am a novice to vmd and I am facing the same problem as in the thread:

www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/21277.html<http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/21277.html>.
As mentioned by Mr.Rajan, I would like to change the atom types to 3 letter code. But kindly provide the information or link to the source code. I am unable to find it.
Thank you for your help in advance.


Revathi.S
M.S. Research Scholar
Indian Institute Of Technology, Madras
India
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