how to prepare a poscar file for dug molecules.

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gaurav · #1 Post by **gaurav** » Fri Aug 01, 2008 1:14 pm

hi everyone.
I am a M.S pharma student currently working on molecular dynamics study of drug molecules using vasp. The poscar file shows only th coordinates of atoms but i dont know how to define the bonds between the atoms in the poscar file. if somebody has worked with molexcules please let me knw it will be of great help to me.

#2 Post by **admin** » Wed Aug 13, 2008 9:47 am

you need not define the bonds in POSCAR. All you have to give is the atoms coordinates (and the box size,...), all the rest is done automactically

gaurav · #3 Post by **gaurav** » Thu Aug 14, 2008 6:35 am

Respected Sir,
Thanks for your valuable suggestion. it helped me a lot. i m facing a problem in submitting the jobs as i dont knw how to specify the length of md run and which parameter defines it.please help me out. Eagerly waiting for your reply

fullerene · #4 Post by **fullerene** » Fri Aug 15, 2008 4:14 pm

INCAR:

IBRION = 0
NSW = nsteps'