Modify Molecule.C to avoid fatal error?

From: George Patargias (gpat_at_bioacademy.gr)
Date: Thu Nov 28 2013 - 02:26:37 CST

• Next message: Norman Geist: "AW: Drifting water molecules"
• Previous message: Axel Kohlmeyer: "Re: Drifting water molecules"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hello

I am sorry to come back to this.

>From a search in the NAMD website and list, I saw that the way to avoid the
following:

FATAL ERROR: child atom x bonded only to child H atoms

is to modify those lines in Molecule.C that contain the statement:

if (atoms[i].mass <=3.5) {

to

if (atoms[i].mass <=2.5) {

In Molecule.C of NAMD 2.9, these lines are 9196 and 9534. Could you please
confirm this?

Thanks again!

George

Dr. George Patargias
Postdoctoral Researcher
Biomedical Research Foundation
Academy of Athens
4, Soranou Ephessiou
115 27
Athens
Greece

Office: +302106597568

• Next message: Norman Geist: "AW: Drifting water molecules"
• Previous message: Axel Kohlmeyer: "Re: Drifting water molecules"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:57 CST