Re: parameter file name

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Sun Sep 10 2006 - 14:53:20 CDT

• Next message: Arturas Ziemys: "Recentering the box on target molecule and wraping"
• Previous message: Anahita Tafvizi: "question regarding the use of reaction coordinate "distance-com" in ABF method"
• In reply to: E. Prabhu Raman: "parameter file name"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hi all,

Here's what was happening. With VDW:

Info: CUTOFF 6.1896e+223

Without VDW:

Info: CUTOFF 2.13032e-313

It turns out that if you have switching off and don't specify a cutoff
distance you can end up with a garbage value that is sensitive to the
state of the memory subsystem.

-Jim

On Fri, 8 Sep 2006, E. Prabhu Raman wrote:

> I observed that when the parameter file name supplied to NAMD has a name comprising of less than 9 characters(excluding the dot and extension), the Vdw potential is not computed i.e the value of that is zero.
> This seems weird as it is difficult to imagine any connection, but I surely observed this.
> Thanks
> Prabhu
>
> E.Prabhu Raman
> Ph.D Student,Bioinformatics & Computational Biology
> George Mason University
>

• Next message: Arturas Ziemys: "Recentering the box on target molecule and wraping"
• Previous message: Anahita Tafvizi: "question regarding the use of reaction coordinate "distance-com" in ABF method"
• In reply to: E. Prabhu Raman: "parameter file name"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:42:35 CST