[gmx-users] density tip3p

[Mark Abraham]

On 1/04/2010 4:58 AM, nishap.patel at 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.patel at utoronto.ca:
>
>> Thanks. I will look up the manual again.
>>
>> Quoting Sander Pronk <pronk at 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.patel at 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
>
>