[gmx-users] Re: lipid.itp and grompp

[Thad Harroun]

Could someone help me summarize the pitfalls of appending a user defined
topology (eg. lipid.itp) to the ffgmx.itp?

ffgmx.itp has sections [defaults] thru all [*types]. So therefore:

A. Including a second [defaults] superceeds the first [defaults] and gives
a grompp warning.

B. A second [atomtypes] section by itself (without subsequent
[nonbond-params]) is okay, and any new non-bonded parameters are
calculated based on the second [defaults] section. The previously read
[nonbond-params] section is retained.(?) No grompp warning. However:

C. A second [nonbond-params] section (typically to include the new atom
types) will cause the first to be ignored, and any non-bonded parameters
not in the explicitly stated second [nonbond-params] section are
calculated based on the second [defaults] section. No grompp warning.

D. B and C also applies to [pairtypes] section.

The best solution is to merge all [*types] sections under one [defualts]
section.

Finally, was it settled that FudgeLJ and FudgeQ were multipliers or
dividers?
 
Thad Harroun 
------------- 
tharroun at ed.ac.uk