[gmx-users] density tip3p

[nishap.patel at utoronto.ca]

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.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