I just checked similar simulations of mine and Berk's suggestion
accounts for similar discrepancies that I notice on a quick evaluation
where g_traj and g_dist fail to give me the same distance as I obtain
from the pull pos.xvg file. As Berk suggests, once I first trjconv
-center -pbc mol -ur compact (giving an appropriate residue for
centering that puts all relevant pulled atoms in the same box) then
g_traj and g_dist both give me the exact same answer as I calculate
based on pull pos.xvg. Chris -- original message -- Hi, 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. Berk
> Date: Thu, 22 Jan 2009 13:22:24 -0500
> From: fied...@umich.edu
> To: gmx-users@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,
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