Justin, I'm a little confused again. Let me put it in a more general way. If I used everything in .pdb and .trr files in reduced units {\sigma}, then gromacs will assume them are in Angstroms, and output in nms (by dividing the input values by 10). That means, the real unit for the output is {\sigma}*10. Is it correct?
Sincerely, Pengzhi On 2/11/13 5:02 PM, Pengzhi Zhang wrote: > Thanks Justin. > > I do use a .pdb file as the topology file, which is also in Angstrom, > not in full format of pdb though (basically atom index ,name and > coordinates). So in my case, gromacs will read all the coordinates in > angstrom? Thus I need to ignore the units nm in output .xvg files. Do I understand it correctly? > No. There is no magic done here. If you provide a .pdb file as input or output to any Gromacs program, that program understands that .pdb files use Angstrom and it processes the coordinates appropriately. All Gromacs tools read and write nm by default, including trajectories (.trr and .xtc) as well as output files from analysis tools (.xvg and others). -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists