[gmx-users] using VMD with GROMACS trajectories

Erik Lindahl lindahl at cbr.su.se
Wed May 16 10:56:04 CEST 2007

Hi Mark,

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.
>> Mark
> This is classic Wiki material... how are we going with this?
> Mark
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