[gmx-users] Decane layer

[M.Naser]

Hi All,

I am still having problem with fixing decane density. I tried with
pressure and I am getting far low density in order to be able the mdrun to
run. Is there anyother parameter I can change to get the right density?


With regards,

Abu



> On Tue, 2005-08-09 at 14:27 +0100, M.Naser wrote:
>> Hi David,
>>
>> It is pure decane density. Could you please describe briefly how to make
>> decane/ water interface. I probably, missing something out.
> Take pure decane, take water as much as you want, translate with
> editconf such that the coordinates do not overlap, merge the files with
> a text editor and run with pressure coupling.
>
>>
>> With regards,
>>
>> Abu
>>
>> > On Mon, 2005-08-08 at 20:32 +0100, M.Naser wrote:
>> >> Thanks david for your reply. I did not expect to get the accurate
>> >> density.
>> >> I wanted 730 kg/m3. I am using following parameter for pressure:
>> >>
>> >> Pcoupl              = Berendsen
>> >> pcoupltype          = isotropic
>> >> tau_p               = 1.0
>> >> compressibility     = 4.5e-5
>> >> ref_p               = 1.0
>> > that's all fine, but the density (you didn't say what you got) depends
>> > on the amount of water and decane of course. 730 g/l sounds low.
>> >>
>> >
>> > --
>> > David.
>> > ________________________________________________________________________
>> > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>> > Dept. of Cell and Molecular Biology, Uppsala University.
>> > Husargatan 3, Box 596,          75124 Uppsala, Sweden
>> > phone:  46 18 471 4205          fax: 46 18 511 755
>> > spoel at xray.bmc.uu.se    spoel at gromacs.org
>> http://xray.bmc.uu.se/~spoel
>> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>> >
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>>
>>
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> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
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