jojo J wrote:
Dear experts,
I posted this message before but I think you did not see it since I
noticed messages after this have been replied. I have a hydrocarbon
Messages do not receive replies in any sort of order. Probably no one has had
any relevant comments yet, or they live in a time zone where they are not awake :)
system with no charged particles. Today In one of the GROMACS tutorials
I saw the following setting in em.mdp file:
fourierspacing = 0.12
;fourier_nx = 0
;fourier_ny = 0
;fourier_nz = 0
;pme_order = 4
;ewald_rtol = 1e-5
;optimize_fft = yes
has been used for PME . Sofar I did not even include coulombtype=PME in
my em.mdp file. What I had was:
constraints = all-bonds
integrator = steep
dt = 0.002 ; ps !
nsteps = 200
nstlist = 10
ns_type = grid
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
;
; Energy minimizing stuff
;
emtol = 1000.0
Can you please guide me whether it is necessary to include these lines
in em file for system having only partial charges like hydrocarbon
(alkane). Also, in md.mdp file I have only coulombtype=PME and not the
This contradicts your statement above. You said you had only uncharged
particles, but clearly this is not the case.
above Ewald settings. Do you recommend to include those settings?
For energy minimization, the effects of plain cutoffs may or may not be
significant. Using plain cutoffs for actual simulation is a bad idea. The
artifacts are well-documented and for modern simulations any good reviewer
should raise an immediate concern if plain cutoffs were used and not thoroughly
justified. A method like PME is significantly more accurate, but you can also
achieve reasonable results using switch, shift, etc. Read about the relevant
mechanics of the force field you're using for what might be appropriate.
Without the mentioned lines I am getting reasonabel results (potential
energy, kinetic, ,, also T coupling works perfectly). If I had better to
unclude them what is the best value for fourierspacing?
I don't think there's ever been any sort of systematic study on the effects of
Fourier grid spacing. The trade-off is between speed and accuracy. Larger
values speed up calculations, but make PME less accurate. Smaller values have
the opposite effect. You could do a small test for yourself (0.12, 0.16,
0.18...) to see if there are any adverse effects.
-Justin
Thank you,
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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