[gmx-users] Re: lipid.itp and grompp
baaden at smplinux.de
Mon Apr 8 12:06:57 CEST 2002
>>> Thad Harroun said:
>> A. Including a second [defaults] superceeds the first [defaults] and gives
>> a grompp warning.
Yes. SHould rather be a fatal error, as if you were changing combination
rules you could get funny results.
>> 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 ! A second [atomtypes] is not ok ! Check it by changing any of the
previous nonbond_params, which will have no effect !
>> 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.
I think that's right.
>> D. B and C also applies to [pairtypes] section.
I don't know :(
>> The best solution is to merge all [*types] sections under one [defualts]
Yes, and to only have ONE single occurrence of atomtypes and nonbond_params in
precisely that order in your whole topology.
Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
mailto:baaden at smplinux.de - ICQ# 11466242 - http://www.marc-baaden.de
FAX/Voice +49 697912 39550 - Tel: +44 1865 275380 or +33 609 843217
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