- Posts: 272
Why is the coordinate jumping?
- xudongh
-
Topic Author
- Visitor
11 years 3 months ago #1339
by xudongh
Why is the coordinate jumping? was created by xudongh
Hi all, (this might not really be a martini question, but I really don't know how to describe it in terms of error in gromacs FAQ list, I apologize for disturbing in advance)
I have a made a gro file of a generic bead polymer that sits on XY axis (including -x and -y) quantity of 50 beads on each axis. but when i do editconf , it generates a new .gro with box file, but the following error occurs
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 specifically the jump of coordinates between bead 174 and 175. This only occured on my -x and -y axis , but not on the +x or +y. (again, all the beads in original gro file is positioned in order next to each other on the axis, such as bead 1, bead 2 bead 3 etc. )
**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
&Why is there jumping occurring? please let me know, thanks
Any input is deeply appreciated.
I have a made a gro file of a generic bead polymer that sits on XY axis (including -x and -y) quantity of 50 beads on each axis. but when i do editconf , it generates a new .gro with box file, but the following error occurs
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 specifically the jump of coordinates between bead 174 and 175. This only occured on my -x and -y axis , but not on the +x or +y. (again, all the beads in original gro file is positioned in order next to each other on the axis, such as bead 1, bead 2 bead 3 etc. )
**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
&Why is there jumping occurring? please let me know, thanks
Any input is deeply appreciated.
Please Log in or Create an account to join the conversation.
- djurre
-
- Offline
- Admin
Less
More
11 years 3 months ago #1340
by djurre
Replied by djurre on topic Why is the coordinate jumping?
Question has been answered at the gromacs mailing list.
Please Log in or Create an account to join the conversation.
Time to create page: 0.098 seconds