[gmx-users] Re: Issue with GROMACS file format
Thanks Justin for your reply. Going by the Gromacs file format: position (in nm, x y z in 3 columns, each 8 positions with 3 decimal places) It is not clear to me as to how many digits before the decimal point can a coordinate column accepts in the Gro file- Is it 3 or 4 digits before the decimal point? (If it is 3 digits before the decimal then there should be a white space between coordinate columns.) Thanks, Satya. -- View this message in context: http://gromacs.5086.n6.nabble.com/Issue-with-GROMACS-file-format-tp4999612p4999649.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Re: Issue with GROMACS file format
On 7/24/12 8:18 AM, SatyaK wrote: Thanks Justin for your reply. Going by the Gromacs file format: position (in nm, x y z in 3 columns, each 8 positions with 3 decimal places) It is not clear to me as to how many digits before the decimal point can a coordinate column accepts in the Gro file- Is it 3 or 4 digits before the decimal point? (If it is 3 digits before the decimal then there should be a white space between coordinate columns.) Theoretically, the .gro format can accept 4 digits before the decimal point (8 total columns, 3 used for after the decimal and one for the decimal point, which leaves 4). The problem in your case is that VMD does not correctly parse the value even though it is technically acceptable within Gromacs. One normally does not deal with coordinates on the order of 1000 nm, so whoever wrote the VMD plugin for changing coordinate file formats probably didn't account for that. -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 * Only plain text messages are allowed! * 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
[gmx-users] Re: Issue with GROMACS file format
Thanks for the reply. In fact, I had followed the fixed format of Gromacs
during the conversion. Below is the sample data, where I have just the
{X,Y,Z}:
2171OHX OW 5231 -0.543 -2.5801000.000
2171OHXHW1 5232 -0.510 -2.5471000.110
Z coordinate is 1000.000 and 1000.110 respectively in the above two lines.
However, in VMD the Z coordinate is read as 000 and and 000.110 which is
then multiplied by a factor of 10 to convert them to A. In VMD, the Z
coordinate is read as 000*10 = 0 and 000.110*10 = 1.10. (Here the decimal
places do not seem to be aligned, but they are aligned in the gro file that
I created).
With Regards,
Satya.
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Re: [gmx-users] Re: Issue with GROMACS file format
On 7/23/12 12:53 PM, SatyaK wrote:
Thanks for the reply. In fact, I had followed the fixed format of Gromacs
during the conversion. Below is the sample data, where I have just the
{X,Y,Z}:
2171OHX OW 5231 -0.543 -2.5801000.000
2171OHXHW1 5232 -0.510 -2.5471000.110
Z coordinate is 1000.000 and 1000.110 respectively in the above two lines.
However, in VMD the Z coordinate is read as 000 and and 000.110 which is
then multiplied by a factor of 10 to convert them to A. In VMD, the Z
coordinate is read as 000*10 = 0 and 000.110*10 = 1.10. (Here the decimal
places do not seem to be aligned, but they are aligned in the gro file that
I created).
While the lines above do follow the prescribed format, perhaps VMD assumes that
there is at least one space between all coordinate entries. Normally one would
not deal with such large quantities in .gro files and all columns are separated
by at least one white space, so you may need to use a different format that can
accommodate large values.
-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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