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 <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: Discussion list for GROMACS users <gmx-users@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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