Dear All,
Recently, I need to use restart2data tool. My Linux system is openSUSE 11.2, and my compiler is gcc. But I don’t know how to compile this tool in my computer.
Can you give me some suggestions? Any advance is welcome.Thank you.
Best,
Yusong He
Dear All,
Recently, I need to use restart2data tool. My Linux system is openSUSE 11.2,
and my compiler is gcc. But I don't know how to compile this tool in my
computer.
you compile it like any other standalone single file c++ code.
did you get any error messages? if yes which ones?
Can you give me some suggestions? Any advance is welcome.Thank you.
have you tried this? g++ -o restart2data.x restart2data.cpp
axel.
Hi axel,
Your command works well, I obtain the executable restart2data successfully, thank you!
And, is there any direct way to convert .pdb file, such as generated by Packmol, into lammps data file?
best,
Yusong
2010/12/16 Axel Kohlmeyer <[email protected]>
Hi axel,
Your command works well, I obtain the executable restart2data successfully,
thank you!And, is there any direct way to convert .pdb file, such as generated by
Packmol, into lammps data file?
yes, using the topotools plugin in VMD.
http://www.ks.uiuc.edu/Research/vmd/plugins/topotools/
but this is not a fully automatic process. depending on
what force field you intend to use, you will have to assign
atom types (they can be strings, topotools will convert them
automatically to suitable numbers on writing and add comments
to the data file to identify them), and may have to "guess" bonds,
angles, dihedrals and so on, as well as assign masses, charges
and other atom properties.
this can all be done with VMD scripting, but requires a little
bit of practice. topotools is written to be complementary to
what typical bio-forcefield topology building tools are good for.
cheers,
axel.