[gmx-users] Decane layer

David spoel at xray.bmc.uu.se
Mon Aug 8 21:29:31 CEST 2005

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 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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