Algorithm used by NAMD

From: Gurpreet Kaur Dhindsa (
Date: Thu Apr 02 2015 - 09:55:36 CDT

Dear all.
I was wondering that NAMD is using only verelt algorithm or it is also coupled with leap frog.

Can anyone tellme that exact which algorithm is used by NAMD software?

Gurpreet Dhindsa

----- Original Message -----

From: "Aron Broom" <>
To: "Gurpreet Kaur Dhindsa" <> Cc: "Namd Mailing List" <>,
Sent: Tuesday, June 17, 2014 10:58:22 AM
Subject: Re: namd-l: Merging the two files......

> Hi Aron,
>It doesn't show me any problem till equilibration. The problem begins when I am using nMoldyn software to
>analyze my data that time time software shows error. Because of that I couldn't analyze it.

You might need to check with the nMoldyn people then and see what convention they use for systems with more than 99,999 atoms. You may then need to do some manipulation on the final output before being able to analyze it.

On Tue, Jun 17, 2014 at 11:44 AM, Aron Broom < > wrote:

and why do you say this is wrong, have you been unable to use it for your next steps?

The PDB format was made with apparently very little (if any) thought towards flexibility. As a result, it has a fixed number of columns for each piece of information, rather than a special separating character. Since 5 columns are given to the atom number you can't go past 99999. So the solution to this is to start using alphabetic characters. I think you'll find that this works fine for your purposes, and only very old programs might have a problem reading those in.

Another problem with these fixed columns is that residue and atom names can only be so many characters, leading to very obfuscated names in many cases, and a lot of unintentional overlap when mixing forcefields.

On Tue, Jun 17, 2014 at 11:00 AM, Gurpreet Kaur Dhindsa < > wrote:

Dear all,
I am trying to merge two different files, one contains 92000 atoms and the other one has
40000 atoms. I am using these commands in VMD
::TopoTools::mergemols [list 1 2]

1,2 are the number of my pdb files in VMD main window.
At the end, I have total of 130000 atoms. VMD gives me the correct atom number till 99000
but after that it starts giving me some type of alphabets.

ATOM 99998 H1 TIP3W5762 -120.414 60.831 - 4.134 0.00 0.00 WT1 H
ATOM 99999 H2 TIP3W5762 -121.121 60.076 -5.310 0.00 0.00 WT1 H
ATOM 186a0 OH2 TIP3W5764 -116.219 60.562 -10.104 0.00 0.00 WT1 O
ATOM 186a1 H1 TIP3W5764 -116.062 60.855 -11.001 0.00 0.00 WT1 H
ATOM 186a2 H2 TIP3W5764 -115.555 61.039 - 9.593 0.00 0.00 WT1 H
ATOM 186a3 OH2 TIP3W5765 -122.951 57.343 13.115 0.00 0.00 WT1 O
ATOM 186a4 H1 TIP3W5765 -122.161 57.022 13.633 0.00 0.00 WT1 H

Can someone try merging the files with that number of atoms? Please give me your suggestions.

Gurpreet Dhindsa.

Aron Broom M.Sc 
PhD Student 
Department of Chemistry 
University of Waterloo 
Aron Broom M.Sc 
PhD Student 
Department of Chemistry 
University of Waterloo 

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