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Molecule order in the Gro File
- jonasori
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7 years 8 months ago #5766
by jonasori
Molecule order in the Gro File was created by jonasori
Hello all,
I've written some code to get an RDF for my Holliday Junction simulations, and am now trying to isolate the 8 phosphates in the middle of the junction. To do that, I am looping through the phosphates (BB1's) and was planning on essentially starting at BB1 #15, taking #15 and #16, skipping 34 (to get to the middle of the next strand), taking those two, and doing the same thing for the next two as well. Essentially, I'm just trying to find the middle two phosphates in each strand.
However, I just wanted to confirm that I understand the ordering correctly; is it correct that in the .gro file, the strands are listed sequentially? For example, it might go [strand1][strand2][strand3][strand4][water][antifreeze][etc.]?
Thanks. I hope I'm not over-wording this question.
Best,
Jonas
I've written some code to get an RDF for my Holliday Junction simulations, and am now trying to isolate the 8 phosphates in the middle of the junction. To do that, I am looping through the phosphates (BB1's) and was planning on essentially starting at BB1 #15, taking #15 and #16, skipping 34 (to get to the middle of the next strand), taking those two, and doing the same thing for the next two as well. Essentially, I'm just trying to find the middle two phosphates in each strand.
However, I just wanted to confirm that I understand the ordering correctly; is it correct that in the .gro file, the strands are listed sequentially? For example, it might go [strand1][strand2][strand3][strand4][water][antifreeze][etc.]?
Thanks. I hope I'm not over-wording this question.
Best,
Jonas
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- peterkroon
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7 years 8 months ago #5769
by peterkroon
Replied by peterkroon on topic Molecule order in the Gro File
The order in your topology file determines the order in the gro file. If these don't match in the beginning you'll get warnings from grompp that atom names do not match.
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