On 1/04/2010 4:58 AM, nishap.pa...@utoronto.ca wrote:
Hello,
So I looked at the manual and I changed my mdp parameters as follows to
equilibrate at a constant pressure.
RUN CONTROL PARAMETERS =
integrator = sd
tinit = 0
dt = 0.002
nsteps = 500000
nstcomm = 1
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 500
nstenergy = 500
nstxtcout = 0
xtc-precision = 1000
nstlist = 5
ns_type = grid
pbc = xyz
rlist = 1.3
coulombtype = pme
rcoulomb = 1.3
epsilon-r = 1
vdw-type = switch
rvdw-switch = 1.0
rvdw = 1.2
DispCorr = EnerPres
fourierspacing = 0.1
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 6
ewald_rtol = 1e-06
epsilon_surface = 0
optimize_fft = no
tc_grps = system
tau_t = 0.1
ref_t = 298
Pcoupl = berendsen
tau_p = 1.0
compressibility = 4.5e-05
ref_p = 1.0
constraints = all-bonds
constraint-algorithm = Lincs
unconstrained-start = no
lincs-order = 4
lincs-warnangle = 30
lincs-iter = 1
gen_vel = yes
gen_temp = 298.0
gen_seed = 173529
I also tried using mdp parameters as mentioned in some of the gromacs
tutorials. I ran this simulation for 1ns and I am still getting density
around 985g/l, which is low for tip3p water (27nm^3, 900 water
molecules). I checked some of the publications and the values they
obtained were ~998g/l. I checked for vacuum in my system, but I didn't
see anything out of the ordinary. Any insights?
Did they use stochastic dynamics?
Have you equilibrated first before collecting your data?
Mark
Quoting nishap.pa...@utoronto.ca:
Thanks. I will look up the manual again.
Quoting Sander Pronk <pr...@cbr.su.se>:
Hi Nisha,
Looking at your .mdp, there are some issues that might lead to the
behavior that you describe:
First: you should try to look up the published densities for tip3p
water at 300K - they might actually be close to what you get.
Second: your neighbor list cut-off (rlist) might be too small to
fully contain the charge groups (check the manual, section 7.3.11).
Third: You haven't enabled long-range mean field correction for the
pressure or energy. Expect the pressure to be strongly dependent on
cut-off (see the same section).
Sander
On Mar 30, 2010, at 22:47 , nishap.pa...@utoronto.ca wrote:
I have a box (3x3x3nm) of Tip3p water molecules ~900 and the
density when I create the box using genbox is 997.177g/l. I did
energy minimization run and the potential energy did converge
smoothly, so I did NPT equilibration run of 100ps and I got the
density value of 975g/l. Why does the density decrease after the
run? these are the parameters that I used :
RUN CONTROL PARAMETERS
integrator = md
tinit = 0
dt = 0.002
nsteps = 50000
nstcomm = 0
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 100
nstenergy = 100
nstxtcout = 0
xtc_precision = 1000
nstlist = 5
ns-type = Grid
pbc = xyz
rlist = 1.1
coulombtype = pme
rcoulomb = 1.1
epsilon-r = 1
vdw-type = switch
rvdw-switch = 0.8
rvdw = 1.0
Tcoupl = V-rescale
tc-grps = System
tau_t = 0.1
ref_t = 300
Pcoupl = berendsen
tau_p = 0.5
compressibility = 4e-05
ref_p = 1.0
constraints = all-bonds
constraint-algorithm = Lincs
unconstrained-start = no
lincs-order = 4
lincs-iter = 1
lincs-warnangle = 30
Am I missing something?
Thanks
Nisha Patel
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Nisha Patel
MSc Candidate
Leslie Dan Faculty of Pharmacy
Department of Pharmaceutical Sciences
144 College Street
Room 1172
Toronto, ON
M5S 3M2
Canada
Telephone: 416-978-1536
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Nisha Patel
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