[gmx-users] Decane layer
mn2 at hw.ac.uk
Mon Aug 8 21:32:29 CEST 2005
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,
> 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
>> tried two ways: 1st I get the editconf to fix the density and then run
>> 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,
>> This e-mail message is subject to http://www.hw.ac.uk/disclaim.htm
>> gmx-users mailing list
>> gmx-users at gromacs.org
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
> 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
> gmx-users mailing list
> gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
This e-mail message is subject to http://www.hw.ac.uk/disclaim.htm
More information about the gromacs.org_gmx-users