[gmx-users] oplsaa force field
mark.abraham at anu.edu.au
Mon Jul 3 01:40:22 CEST 2006
The answers to both of these questions are in the comments in
src/kernel/toppush.c, in function push_at(). I found them grepping
src/*/*.[ch] for scanf (the C function you'd use to read up these files)
and looking for topology-related filenames...
> I'd like to use oplsaa FF format to build my own force field for my
> project. After I finished it, I can use pdb2gmx. but not grompp. The
> problem is from my **nb.itp file. I have specified some unusual (not
> follow the combination rule) nonbonded interaction parameters after
> [ atomtypes ] section as follows:
> [ nonbond_params ]
> ; i j func sigma epsilon
> CT CT 1 3.80000e-01 2.09200e-01
> When I run grompp, the program complains that atom type CT is not found.
> If I change CT to opls_182, then it works fine. However, when I check
> oplsaabon.itp, CT is used, but not opls_182. Could anyone tell me why I
> can't use atom type in *nb.itp? How can I fix it? If opls_182 is defined
> as atom type, then how does gromacs recognize CT is **bon.itp?
OPLS/AA appears to use different names for bonded and non-bonded atom types.
See line 172 of the above file.
> By the way, my question relates to my previous question. Unfortunately,
> no one answered it. I really appreciate someone can help me. The
> following is my previous email:
> In ffoplsaanb.itp, there are 8 columns.
> ; name bond_type mass charge ptype sigma epsilon
> opls_001 C 6 12.01100 0.500 A 3.75000e-01
> 4.39320e-01 ; SIG
> In ffG53a5nb.itp, there are 7 columns.
> [ atomtypes ]
> ;name at.num mass charge ptype c6 c12
> O 8 0.000 0.000 A 0.0022619536 1e-06
> Could anyone tell me how gromacs knows to read 8 columns for oplsaa FF,
> but 7 columns for gromos FF? Thanks!
The algorithm is described just below in that file too.
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