VMD-L Mailing List

From: Nicolas Bigaouette (nbigaouette_at_gmail.com)
Date: Thu Jul 31 2008 - 18:33:26 CDT

I have create some .gro which looks like this:
[...]
1E E 2 0.000 0.200 0.200 0.0000 0.0000 0.0000
[...]
But when I import them in VMD, the position are multiplied by 10, so it is
(0,2,2) instead of (0,0.2,0.2)

It did not happen with other file format (VTF). I checked the source, and to
my surprise there is a comment at the begining of Gromacs.h:
 * o gro_rec() assumes positions in .gro files are nanometers and
 * converts to angstroms, whereas they really could be any unit
and a couple of lines later, there is a degine:
#define ANGS_PER_NM 10

Why is it converting the file's value?? If the data file is wrong, then I
prefer changing it myself then having to hack VMD's code to remove the
scaling factor. The file says 0.2, I want to see 0.2 in VMD.

I did a patch to change that:

--- plugins/molfile_plugin/src/Gromacs.h.orig 2008-07-31
19:26:41.000000000 -0400
+++ plugins/molfile_plugin/src/Gromacs.h 2008-07-31 19:27:11.000000000
-0400
@@ -96,8 +96,10 @@
 #define MAX_G96_LINE 500 // Maximum line length of .g96 files
 #define MAX_TRX_TITLE 80 // Maximum length of a title in .trX
 #define MAX_MDIO_TITLE 80 // Maximum supported title length
-#define ANGS_PER_NM 10 // Unit conversion factor
-#define ANGS2_PER_NM2 100 // Unit conversion factor
+//#define ANGS_PER_NM 10 // Unit conversion factor
+//#define ANGS2_PER_NM2 100 // Unit conversion factor
+#define ANGS_PER_NM 1 // Unit conversion factor
+#define ANGS2_PER_NM2 1 // Unit conversion factor

 // All the supported file types and their respective extensions