[gmx-users] Decane layer

[M.Naser]

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


Thanking you again,

Abu

> On Mon, 2005-08-08 at 18:11 +0100, M.Naser wrote:
>> Hi All,
>>
>> Currently I am having problem with creating decane water interface. I
>> have
>> tried two ways: 1st I get the editconf to fix the density and then run
>> the
>> mdrun. the mdrun chrashed because of the bad contact. I minimised the
>> energy and was not helpfull. Then, I tried coupling pressure and it did
>> not work as well. When I get the right density mdrun crashes and when I
>> increase the box size mdrun runs ok but I can not get the right density.
>> Is there any solution of this problem?
>>
> What is the right density, and which do you get with pressure coupling?
> Don't expect to be more accurate than a few percent.
>> With regards,
>>
>> Abu
>>
>>
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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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