Project

General

Profile

Bug #39

Generation of initial velocities counts dummy atoms as normal atoms.

Added by Ramon Garcia almost 14 years ago. Updated almost 14 years ago.

Status:
Closed
Priority:
High
Assignee:
Erik Lindahl
Category:
mdrun
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
Close

Description

When grompp generates initial velocities, it counts all the atoms for the
evaluation of the total kinetic energy. Dummy atoms should not be counted.
Because of this, simulations containing water models with dummy atoms such as
TIP4P, start with a temperature higher than the expected one. In particular, in
a simulation of water with the van der Eerden model (which has the same number
of dummy atoms and real atoms), the initial temperature is exactly twice the one
the user specified in grompp.mdp .

grompp.c.diff (916 Bytes) grompp.c.diff Modification of grompp.c Ramon Garcia, 12/30/2005 06:51 PM

History

#1 Updated by Ramon Garcia almost 14 years ago

Created an attachment (id=9)
Modification of grompp.c

Go to the directory where grompp.c resides and run

patch < this_patch

#2 Updated by Erik Lindahl almost 14 years ago

Proposed fix has been added to both CVS branches. Thanks!

Also available in: Atom PDF