On 12/31/12 5:40 PM, Xu Dong Huang wrote:
Dear Justin,
(here is the picture of the molecule after editconf, note the negative x and
negative y axis is missing the rest of the beads that is suppose to be like the
positive x and positive y)
http://i1284.photobucket.com/albums/a571/X_huang1/ScreenShot2012-12-31at53618PM_zpse5f421f1.png
*Even though according to the .gro coordinates, those beads of 175 and up are
jumped, i don't see the relocated beads anyhow in this VMD viewing. I'm so
confused of what is happening.
Is your .gro file valid? Specifically, does the second line of the input file
specify the correct number of atoms? Does the output file have the same number
of atoms as the input? That is the only reason I know of for a file being
truncated.
-Justin
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu
On Dec 31, 2012, at 5:31 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 12/31/12 4:53 PM, Xu Dong Huang wrote:
Dear advanced gromacs users,
I have created an arbitrary molecule .gro file containing coordinates of my
martini-beads. basically, there are 50 beads sitting on each axis of (x,y, -x
and -y) forming like a cross. (Each bead with distance 0.43). However, when I
try to use editconf on my .gro file to generate a box (editconf -f star.gro -o
star_box.gro -c -d 1.0 -bt cubic) , it gives me back a new .gro file with a bad
molecule. In VMD viewing, I see that the negative axis part of my molecules are
cut off. Closer inspection shows the following for a particular segment of the
molecule coordinates:
**original .gro coordinates:
1star O1 170 0.000 -8.170 0.000
1star O1 171 0.000 -8.600 0.000
2star O2 172 0.000 -9.030 0.000
2star O2 173 0.000 -9.460 0.000
2star O2 174 0.000 -9.890 0.000
2star O2 175 0.000 -10.320 0.000
2star O2 176 0.000 -10.750 0.000
2star O2 177 0.000 -11.180 0.000
2star O2 178 0.000 -11.610 0.000
2star O2 179 0.000 -12.040 0.000
2star O2 180 0.000 -12.470 0.000
2star O2 181 0.000 -12.900 0.000
2star O2 182 0.000 -13.330 0.000
2star O2 183 0.000 -13.760 0.000
*new .gro coordinates:
1star O1 169 12.421 4.681 16.695
1star O1 170 12.421 4.251 16.695
1star O1 171 12.421 3.821 16.695
2star O2 172 12.421 3.391 16.695
2star O2 173 12.421 2.961 16.695
2star O2 174 12.421 2.531 16.695
2star O2 175 12.421 22.741 16.695
2star O2 176 12.421 23.171 16.695
2star O2 177 12.421 23.601 16.695
2star O2 178 12.421 24.031 16.695
2star O2 179 12.421 24.461 16.695
2star O2 180 12.421 24.891 16.695
2star O2 181 12.421 25.321 16.695
2star O2 182 12.421 25.751 16.695
2star O2 183 12.421 26.181 16.695
Notice the jump on atom number 174 and 175, why is there a sudden coordinate
jump?
All i can see in VMD is my negative axis part of the molecule beads are cut off.
editconf builds boxes from the coordinate origin so that there are never negative
coordinates. It should be able to deal with those coordinates, equally shifted, which it
appears they were. Can you provide images of what's going on? I don't clearly
understand what's wrong. What do you mean by "cut off?" Nonexistent?
Incorrectly placed?
-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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========================================
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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