that's a good idea to just do a single energy calculations on the structures
minimized by the other program although i am already cringing at the thought
of file formatting.
is there an elegant way of just doing an energy calculations in gromacs? the
only way i can think of right now is by setting the nstep = 0 in the em.mdp.
thank you for your help.
rob
From: Mark Abraham <[EMAIL PROTECTED]>
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To: Discussion list for GROMACS users <[email protected]>
Subject: Re: [gmx-users] grompp single vs double precisions
Date: Sat, 04 Mar 2006 12:13:51 +1100
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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
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