[gmx-users] density tip3p

[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