On 4/25/13 10:05 AM, Dr. Vitaly Chaban wrote:
PME should NOT be used with charged systems, for obvious reasons.
FYI Gromacs provides a neutralizing background charge.
http://comments.gmane.org/gmane.science.biology.gromacs.user/639
There may, of course, be issues with the physical reality of such a setup, but
this is a common question.
-Justin
On Thu, Apr 25, 2013 at 4:00 PM, ABEL Stephane 175950
<stephane.a...@cea.fr>wrote:
And ? sorry but i do not understand...
Stephane
------------------------------
Message: 2
Date: Thu, 25 Apr 2013 15:39:12 +0200
From: "Dr. Vitaly Chaban" <vvcha...@gmail.com>
Subject: Re: [gmx-users] Martini with PME, temp two low
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
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Hmmm....
Aren't the keywords here "charged system" + "PME"?
Dr. Vitaly Chaban
On Thu, Apr 25, 2013 at 1:34 PM, XAvier Periole <x.peri...@rug.nl> wrote:
Did you visualise the system? T in function of time? Epot in function of
time?
As a side note (not relevant for PME) the mix of nstlist = 10 and the
rlist = 1.0 is pretty bad! You want at least rlist=1.2 when nstlist=5 and
rlist=1.4 if nstlist =10.
On Apr 25, 2013, at 1:10 PM, ABEL Stephane 175950 <stephane.a...@cea.fr>
wrote:
Hello all,
I am trying to test the martini force field with PME for a charged
system that contains na+, water, surfactant, octane molecules at 298K and
P=0.1MPa. My system works well, if i use the standard shift parameters
(correct temp, and pressure). But for for the simulation with PME , the
temp of the system decrease to 290 K. Below my *.mdp parameters for a
NPT
equil at 298K
integrator = md
dt = 0.020
nsteps = 10000 ; 200ps
nstcomm = 10
comm-grps =
;refcoord_scaling = com
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000
nstenergy = 100
;nstxtcout = 1000
xtc_precision = 100
;xtc-grps =
energygrps = AOT W ION OCT
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.
; PME parameters
coulombtype = PME
rcoulomb = 1.2
rvdw = 1.2
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
tcoupl = v-rescale
tc-grps = AOT_W_ION OCT
tau_t = 1.0 1.0
ref_t = 298 298
Pcoupl = berendsen
Pcoupltype = isotropic
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
;gen_vel = no
;gen_temp = 0
;gen_seed = 473529
; MARTINI and CONSTRAINTS
; for ring systems and stiff bonds constraints are defined
; which are best handled using Lincs.
constraints = none
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 3
Results obtained with W/ PME
Statistics over 10001 steps using 1001 frames
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Coul.
recip.
1.63789e+04 1.25195e+03 -4.02093e+05 -8.22079e+03
-4.86843e+04
Potential Kinetic En. Total Energy Temperature Pressure
(bar)
-4.41367e+05 7.81801e+04 -3.63187e+05 2.90373e+02
-1.76470e+01
T-AOT_W_ION T-OCT
2.90629e+02 2.90357e+02
Results W:o PME
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR)
Potential
1.60482e+04 1.24820e+03 -3.34608e+05 -7.33665e+02
-3.18046e+05
Kinetic En. Total Energy Temperature Pressure (bar)
8.02685e+04 -2.37777e+05 2.98129e+02 -3.07123e+01
Box-X Box-Y Box-Z
1.52926e+01 1.52926e+01 1.52926e+01
T-AOT_W_ION T-OCT
2.98141e+02 2.98129e+02
Did I miss something ?
Note that for the moment i do not use the polarizable water model.
Thanks for your help
Stephane
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Research Scientist
Department of Biochemistry
Virginia Tech
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