[gmx-users] grompp single vs double precisions

[Mark Abraham]

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. 

Have you looked at the resulting structures to see if you are comparing 
the same states? Watching the minimization "trajectories" will help you 
assess what differences there may be. Ordinarily I would pick a 
structure minimized with one program and then just do an energy 
calculation on the other, if I wanted to do this sort of calculation. 
It's quite similar to what quantum chemists do all the time - get 
geometries at one "level of theory" and then calculate energies at 
another more expensive one whose cost is prohibitive for optimization.

> 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?

I doubt single/double mdrun will matter to you for geometry 
optimization. I don't know if double grompp is necessary to make double 
mdrun effective - my guess would be not 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:

It looks unremarkable.

Mark