[gmx-users] grompp single vs double precisions

Sat Mar 4 22:28:27 CET 2006

i am using twin range cut-off instead of PME to do the minimization. i could 
try PME to see if it changes anything. i'll also compile the double version 
of grompp to try everything. thank you very much.

rob

>From: Yang Ye <leafyoung81-group at yahoo.com>
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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 13:16:28 +0800
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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. 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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