[gmx-users] Decane

[M.Naser]

Hi David,

Still crashing. I tried even genconf -dist 2 2 2.

With regards,

Abu

> On Mon, 2005-08-29 at 17:41 +0100, M.Naser wrote:
>> Hi David,
>>
>> Yes, it was inside the box. I going to try with genconf.
> the box needs to be 0.4 nm larger than the molecule in all dimensions to
> prevent bad contacts.
>>
>> 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
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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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