[gmx-users] using VMD with GROMACS trajectories
lindahl at cbr.su.se
Wed May 16 10:56:04 CEST 2007
David was installing a new server - as soon as I get an IP for it
I'll enter it in the gromacs DNS and we can put a wiki online :-)
David - any update?
On May 16, 2007, at 10:51 AM, Mark Abraham wrote:
> Mark Abraham wrote:
>> Roughly speaking, a gromacs .top file has the same sort of
>> information as a .psf file, but VMD won't read one natively.
>> Instead, give VMD a structure file (.gro, .g96, .pdb or anything
>> else) that corresponds (in the same order) to the atoms that are
>> saved in your trajectory in place of the .psf file, and then load
>> the trajectory (.trr or .xtc) into that molecule in the same way
>> you would a .dcd file (see the VMD manual if you don't understand
>> this step). VMD will guess the atom connectivity based on the
>> original structure you give it - you should not expect this
>> connectivity to correspond perfectly to that in your .top file.
>> The gromacs tool ngmx can do a rough and ready visualization, if
>> the right X libraries exist and ngmx was installed. See "man ngmx"
>> for info.
> This is classic Wiki material... how are we going with this?
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