[gmx-users] grompp single vs double precisions

[Yang Ye]

rob yang wrote:
> 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 conformations.
> 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
When you refer this rcoulomb as long range, do you mean to use PME. You 
did not have this option in the mdp.
> rvdw                =  1.4 ;long range
> ;
> ;       Energy minimizing stuff
> ;
> emtol               =  1
> emstep              =  0.001
> nstcgsteep          =  10
>
>
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