[gmx-users] grompp single vs double precisions

[rob yang]

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 <Mark.Abraham at anu.edu.au>
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>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>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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