Results (14)

GROMACS Feature #2579 (New): Add dimensionality option to gmx trjconv -center
gmx trjconv -center centers a box in all 3 dimensions. For aniso ... n, while not impacting the lateral positions. 07/19/2018 04:53 PM
GROMACS Bug #2230 (Closed): gmx density hangs when computing charge density with -symm
gmx density hangs when computing charge densi ... tems without shells this option works well. 08/11/2017 11:48 AM
GROMACS Bug #2171 (Closed): editconf -h indicates -center defaults to (0,0,0) but that is not true from a user perspective
gmx editconf -c deaults to centering the sele ... nates of the geometrical center": <pre> -center <vector> (0 0 0) Coord ... is not a useful default value as providing "-center" without any numbers gives an error: <pre ... b.gro -n index.ndx -o sel_and_center.gro -c -center --------------------------------------- ... mmand-line options In command-line option -center Too few (valid) values For more info ... 0,0,0) is neither a useful default value if "-center" is provided on its own, nor it is the value used for the center when "-center" is not provided at all with -c like this: ... ual performance is what one would desire. 05/05/2017 09:07 PM
GROMACS Task #1781 (Accepted): re-design benchmarking functionality
mdrun counter reset does not interaction well ... water box (but that is likely not relevant). 07/16/2015 12:19 AM
GROMACS Bug #1698 (Closed): g_density -center shifts coordinates in the wrong direction
in gmx_density.c in the function center_coor ... e the density profile using g_density option -center, then use trjconv to shift the system 1 nm along z and run g_density -center again. Instead of getting the same result as ... n the wrong direction). Thank you, Chris. 03/04/2015 07:57 PM
GROMACS Bug #1592 (Rejected): Manual of trjconv is unclear about precision.
The manual says: The precision of .xtc and ... be written with different number of decimals. 09/07/2014 09:42 AM
GROMACS Feature #1168 (In Progress): g_density does n ... n PBC over z and constant pressure simulation
The problem is that g_density builds up a his ...;cid=1362008104264-151 This ... his plus the unexpected behaviour of trjconv -center can lead to a fair amount of spread/flatteni ... s the COM and not the location of (max-min)/2 02/28/2013 01:35 AM
GROMACS Feature #1167 (New): trjconv -center would be more intuitive if it centered the c ... e midpoint between minimum and maximum values
I have included a patch that changes trjconv 4.5.3 so that the -center option now acts on the center of mass of the ... ter-intuitive centering behaviour of trjconv -center still exists in version 4.6. I originally ... 02/28/2013 12:39 AM
GROMACS Feature #871 (Closed): request for trjconv -box to allow modification of only one or two dimensions
It would be nice if trjconv -box -1 -1 14 wou ... to frame. Thus, I could do this: trjconv -center -pbc mol -f a.xtc -o b.xtc trjconv -box -1 ... as larger than the z in any frame) trjconv -center -pbc none -f c.xtc -o d.xtc In the second ... rue unless you have already modified trjconv -center to act on the center of mass instead of (max ... trjconv to do that. Thank you, Chris. 01/30/2012 05:16 PM
GROMACS Bug #526 (Closed): trjconv option inconsistency
trjconv sometimes requires a supporting input ... ead and 4.0.7 both have the faulty behaviour. 08/26/2010 03:52 PM