[gmx-users] Decane

[M.Naser]

Hi David,

Yes, it was inside the box. I going to try with genconf.

With regards,

Abu

> On Mon, 2005-08-29 at 17:30 +0100, M.Naser wrote:
>> Hi Erik,
>>
>> Thanks for your reply. I was trying to get a decane box of 730kg/cm^3. I
>> started with dec50.gro file from the pakage. I took just one molecule
>> from
>> the file and put the molecule in reletively bigger box that is 2 2 2 nm
>> using editconf to avoid bad contact. Then, using genbox I fill a box of
>> 30
>> 30 10 nm with the decane molecule. Then I run mdrun using pressure
>> couple
>> to get the desired density. When I run with constraint after a few ps
>> run,
>> it starts producing a lot of pdb files but when I run with no constrain
>> it
>> woks perfectly well. By the way, I have  tried with both algorithm :
>> SHAKE
>> and LINCS.
> is the decane molecule completely inside the 2 2 2 box?
> You may want to use genconf rather than genbox.
>>
>> With regards,
>>
>> Abu
>>
>> > Hi,
>> >
>> > That's impossible to say without more information - please post the
>> > explicit error message!
>> >
>> > Cheers,
>> >
>> > Erik
>> >
>> > On Aug 29, 2005, at 5:40 PM, M.Naser wrote:
>> >
>> >> Hi All,
>> >>
>> >> I have been wondering why my simulation of decane crashing with all-
>> >> bond
>> >> constrain?
>> >>
>> >> Thanks in advance,
>> >>
>> >> 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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