Re: PCA calculation

From: Richard Wood (
Date: Tue Feb 12 2008 - 09:57:42 CST

What gets me in this thread is the "implication" that one has to be able to write code in order to do MD, use NAMD, do PCA or, better yet, even be a computational chemist.

Personally, I'd rather know why H2O is a liquid and H2S isn't than to be able to "write code".

A person that knows why water is a liquid when it shouldn't be is a chemist (or physicist) while the latter is a programmer.

Those of you that want to imply we should all be able to write code should go and be on another list.

A REAL chemist uses the code (or program) that helps him to be solve the particular problem he's working on or is interested in.

We're not all programmers on this list.

Good grief.

I've done PCA and I used NAMD to do my MD and used a script written in Matlab.

Richard L. Wood, Ph. D.
University of Minnesota
Dept. of Medicinal Chemistry,
College of Pharmacy
717 Delaware St. SE
Minneapolis, MN 55414-2959

----- Original Message ----
From: Peter Freddolino <>
To: "Xu, Jiancong" <>
Cc: ramya narasimhan <>;
Sent: Monday, February 11, 2008 10:38:15 AM
Subject: Re: namd-l: PCA calculation

*Real* programmers use matdcd
( and do it in
matlab. ;-)
But gromacs is the fast and easy way way.

Xu, Jiancong wrote:
> Don't think so. One thing you can do is to convert dcd trajectory to any other format that can be read by gromacs, and use gromacs to calculate PCA.
> Jiancong
> -----Original Message-----
> From: on behalf of ramya narasimhan
> Sent: Mon 2/11/2008 2:49 AM
> To:
> Subject: namd-l: PCA calculation
> Hi all,
> Is it possible to calculate PCA for MD trajectories using NAMD?
> Thanks in advance.
> Ramya.L.
> ---------------------------------
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