[gmx-users] grompp single vs double precisions

rob yang nextgame at hotmail.com
Sat Mar 4 00:04:38 CET 2006

hi list,
i am comparing the relative energy differences between different 
conformations of a same molecule in vaccuum. i am using both gromacs and 
another software to compare the results. the forcefield for both softwares 
is oplsaa (2001), and i've manually verified that they are indeed the same 
for my molecule as well as the partial charges.
the relative energy results obtained from these 2 softwares are different. i 
understand that different softwares have different implementations but i 
think i should be able to get a similiar relative energies for these 
so i am thinking maybe the minimizations is where things went wrong. i have 
compiled the double version of mdrun. but i didn't for grompp since i didn't 
think it was necessary. the question i have for you guys is then: is the 
double version of grompp also necessary?

what other insights do you guys have to the differences? thank you very 
much. i'll also present the em.mdp i used below:
title		    = em
cpp                 =  /lib/cpp
define              =  -DFLEXIBLE
constraints	    = none
integrator          =  cg
dt		    = 0.002
nsteps              =  100000
nstlist             =  10
ns_type             =  grid
rlist               =  0.8 ;short range
rcoulomb            =  1.4 ;long range
rvdw                =  1.4 ;long range
;       Energy minimizing stuff
emtol               =  1
emstep              =  0.001
nstcgsteep          =  10

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