[gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance
gmx3 at hotmail.com
Thu Jan 22 22:55:16 CET 2009
There could be a problem with periodic boundary conditions.
Do you have multiple molecules in a pull group, or broken molecules?
In that case the COM position of 3.3.3 and g_traj are both incorrect.
The pull code in 4.0 grompp and mdrun are (as far as I know) always correct.
> Date: Thu, 22 Jan 2009 13:22:24 -0500
> From: fiedler at umich.edu
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance
> Dear all,
> I have encountered an odd behavior with use of the "pull_geometry =
> distance" option of the pull code, upon transitioning from Gromacs
> version 3.3.3 to version 4.0.3. It appears to be related to the center
> of mass distances of the two pull groups, which has an effect of
> abruptly displacing the coordinates of the less massive group. A
> diagnostic is a discrepancy between the distances between the pull
> groups from the preprocessor output in version 4.0.3, and the distance
> between the groups as calculated using the difference of the groups'
> centers of mass from the g_traj utility. For example, using the
> coordinates of a system previously equilibrated with the constraint
> force approach from version 3.3.3, the grompp output from version 4.0.3 is:
> Pull group natoms pbc atom distance at start reference at t=0
> 0 2672 1336
> 1 60 6818 2.673 0.400
> Using g_traj (4.0.3 version), the difference of the distance between the
> center of masses of the two groups is: 0.39911 nm versus the 2.673 value
> from above.
> This issue does not exist in previous versions of Gromacs including
> version 3.3.3. In version 4.0.3, this behavior occurs for both
> pull=umbrella and pull = constraint, on 32 and 64 bit architecture
> systems, and in both single and double precision calculations. A test
> of a two atom system determined that the pull_start option was not
> appropriate. The pull options used in the mdp file are listed below, as
> well as the contents of the ppa file which has worked previously.
> Suggestions would be appreciated,
> Thank you,
> Steve Fiedler
> Gromacs 4.0.0 mdp pull options
> pull = constraint
> pull_geometry = distance
> pull_dim = N N Y
> pull_start = no
> pull_init1 = .4
> pull_group0 = Ref
> pull_group1 = Buk
> Gromacs 3.3.3 ppa file:
> runtype = constraint
> group_1 = BUK
> reference_group = Ref
> reftype = com
> constraint_direction = 0 0 1
> constraint_distance1 = 0.400
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