Hi
I am using this tool for the first time. I am not able to figure out the number that I should put in for mol? Like in lmpbondsfromdata [molinfo top] data.micelle, is it the molecular id that appears first? I put 1 and it seemed to work, but then I restarted it and it’s not working it seems, then I put 0, and it calculated all bonds exactly as 3035, but the picture generated is not correct it seems( I have attached it herewith). I have 15 polymer chains and 850 solvent molecules of water and methanol in my system.
Any comment will be appreciated.
Thanks
Chetan
Hi
I am using this tool for the first time. I am not able to figure out the
number that I should put in for mol? Like in lmpbondsfromdata [molinfo top]
please ask questions about VMD on the VMD mailing list.
but in this case i can save you the time and suggest that
you first spend some time to understand how the script interface
in VMD works and how you address molecules. to explain this
in detail here would be redundant and go too far. VMD has
good documentation and great tutorials.
data.micelle, is it the molecular id that appears first? I put 1 and it
seemed to work, but then I restarted it and it's not working it seems, then
I put 0, and it calculated all bonds exactly as 3035, but the picture
generated is not correct it seems( I have attached it herewith). I have 15
polymer chains and 850 solvent molecules of water and methanol in my system.
sorry, but the picture _is_ correct. it is showing the
bonds how they are defined in the data file. the long bonds
going across the simulation cell are due to molecules that
stretch across periodic boundaries. you saved coordinates
without unwrapping them or used a file format where VMD does
not recognize this.
cheers,
axel.