[gmx-users] grompp

[Dallas B. Warren]

> I am running grompp for a pure lipid system and grompp
> gives me the error that:
> 
> number of coordinates in coordinate file
> (96_neatsys14.gro, 19926) does not match topology 
> (96_neatsys14.top, 13014)
> 
> I found out that the total 6912 atoms (19926-13014)
> that grompp is not taking are the Hydrogens attached
> to the 96 DMPC lipids. 
> 
> Can I keep these hydrogens with me since for lipids
> united atoms approach might not help? Can I
> incorporate OPLS forcefeild somehow into it?

Not entire clear what you are doing here, but you cannot (or may be more
correctly it is very bad form to and you will have great difficulty
justifying doing so to reviewers) use two different forcefields together
within the same simulation.

Reason for that is that the forcefield parameters are generated
"together" as a set to give the correct properties.  Mixing another
forcefield in will mean that the interactions occuring are unlikely to
be consistent and "correct:".

So you need to stick to the one forcefield.

Catch ya,

Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9524
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail.