Rolf Erwin Isele-Holder wrote:
Dear users,
I'm running a simulation which uses ethanol as solvent. When using g_hbond the
programm is able to recognize the solute's donors and acceptors, however it
does not recognize any acceptors or donors of ethanol. Here is a part of my
topology:
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB
chargeB massB
1 HO 1 ETHH EH 1 0.398 1.008 ; qtot
0.398
2 OA 1 ETHH EO 1 -0.548 15.9994 ; qtot
-0.15
3 CH2 1 ETHH EC1 1 0.15 14.027 ; qtot 0
4 CH3 1 ETHH EC2 2 0 15.035 ; qtot 0
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
2 3 1
3 4 1
Why doesn't g_hbond recognize any donors or acceptors?
See g_hbond -h. The recognition is based on the atom name, and this
conventionally doesn't start with E, as in your case. You will need to
change the atom names in your initial coordinate file and topology,
regenerate your .tpr, and then attempt the analysis. The trajectory is
fine, since it has no atom names. Just keep the atom order the same!
Mark
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
