[gmx-users] reduced units
Hello there, I'm a gromacs newbie. I am using gromacs function g_anaeig to do principle component analysis. I use coordinates (converted to be .trr files for gromacs) and topology from amber. I know that gromacs works with units like nm, kJ/mol etc, while amber with angstrom. Does anyone know that when gromacs read the coordinate files, whether it assumes the values are in nm or in angstrom (if so, gromacs converts them by itself to nm without telling us)? Thanks for any help. Sincerely, Pengzhi -- gmx-users mailing listgmx-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
RE: [gmx-users] reduced units
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? Sincerely, Pengzhi On 2/11/13 4:09 PM, Pengzhi Zhang wrote: Hello there, I'm a gromacs newbie. I am using gromacs function g_anaeig to do principle component analysis. I use coordinates (converted to be .trr files for gromacs) and topology from amber. I know that gromacs works with units like nm, kJ/mol etc, while amber with angstrom. Does anyone know that when gromacs read the coordinate files, whether it assumes the values are in nm or in angstrom (if so, gromacs converts them by itself to nm without telling us)? Gromacs uses nm for everything except when a .pdb file is specified for input or output, in which case Angstrom is used. -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 listgmx-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
RE: [gmx-users] reduced units
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
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RE: [gmx-users] reduced units
In my case, all the related units are about length, so I won't consider
temperature, charge etc.
Here is the confusion.
On one hand, from the above discussion: If the input is from the .pdb file,
which is in reduced units ( {\sigma}=3.8 Angstrom), as well as the
coordinate file, the program g_covar reads the coordinates in Anstroms and
convert them to nms, then gives an output of all the eigenvalues of the
covariance matrix, in units of nm^2, for example, the first eigenvalue given
is 5.5 nm^2. So mapping to the correct reduced units, I think I need to
change the nm^2 to ({\sigma}*10)^2=1444 Angstrom^2, thus the first
eigenvalue is 550 {\sigma}^2, i.e. 7942 Angstrom^2.
On the other hand, per to the manual, the output should be anyway 5.5
{\sigma}^2 although written in 5.5 nm^2 in the .xvg file, as if gromacs does
no unit-conversion here at all, even a .pdb file is given as input.
The latter gives values of better sense from my actual example.
Sincerely,
Pengzhi
On 2/11/13 5:26 PM, Pengzhi Zhang wrote:
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?
If your input is in reduced units, then so too is the output, per manual
section 2.3. Perhaps you can provide an actual example of whatever is
causing your confusion.
-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
--
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