Hi Nisha,
I have performed a benchmark simulations of TIP3P water and I still obtained density 0.984g.cm-3. It looks that this model gives such a density. If you look at JCP 79, 926, 1983 you will see that the authors got 0.982g.cm-3 with MC. (Table 3) Try to evaluate alsoo other properties, each model of water has some deficiencies. I tried large number of cut-offs combinations LJ and QQ tyoes of interactions, but the density did not gange by more than 0.001g.cm-3.
Greetings
Zuzana
Dňa 03/31/10, nishap.pa...@utoronto.ca napísal:
I have performed a benchmark simulations of TIP3P water and I still obtained density 0.984g.cm-3. It looks that this model gives such a density. If you look at JCP 79, 926, 1983 you will see that the authors got 0.982g.cm-3 with MC. (Table 3) Try to evaluate alsoo other properties, each model of water has some deficiencies. I tried large number of cut-offs combinations LJ and QQ tyoes of interactions, but the density did not gange by more than 0.001g.cm-3.
Greetings
Zuzana
Dňa 03/31/10, nishap.pa...@utoronto.ca napísal:
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?
Thanks
Nisha P
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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