[gmx-users] Decane
David van der Spoel
spoel at xray.bmc.uu.se
Mon Aug 29 23:22:29 CEST 2005
On Mon, 2005-08-29 at 19:04 +0100, M.Naser wrote:
> Hi David,
>
> Still crashing. I tried even genconf -dist 2 2 2.
Check your topology (or try attached from GROMACS test set).
>
> 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
> >> >> >>
> >> >> >>
> >> >> >> __________________________________________________________________
> >> >> >>
> >> >> >> DISCLAIMER:
> >> >> >>
> >> >> >> This e-mail message is subject to http://www.hw.ac.uk/disclaim.htm
> >> >> >> __________________________________________________________________
> >> >> >>
> >> >> >> _______________________________________________
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> >> >> >>
> >> >> >>
> >> >> >
> >> >> > _______________________________________________
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> >> >> >
> >> >>
> >> >>
> >> >>
> >> >> __________________________________________________________________
> >> >>
> >> >> DISCLAIMER:
> >> >>
> >> >> This e-mail message is subject to http://www.hw.ac.uk/disclaim.htm
> >> >> __________________________________________________________________
> >> >>
> >> >> _______________________________________________
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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
> >> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >> >
> >> >
> >> > _______________________________________________
> >> > gmx-users mailing list
> >> > gmx-users at gromacs.org
> >> > http://www.gromacs.org/mailman/listinfo/gmx-users
> >> > Please don't post (un)subscribe requests to the list. Use the
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> >> >
> >>
> >>
> >>
> >> __________________________________________________________________
> >>
> >> DISCLAIMER:
> >>
> >> This e-mail message is subject to http://www.hw.ac.uk/disclaim.htm
> >> __________________________________________________________________
> >>
> >> _______________________________________________
> >> gmx-users mailing list
> >> gmx-users at gromacs.org
> >> http://www.gromacs.org/mailman/listinfo/gmx-users
> >> 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.
> > ________________________________________________________________________
> > 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
> > http://www.gromacs.org/mailman/listinfo/gmx-users
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> >
>
>
>
> __________________________________________________________________
>
> DISCLAIMER:
>
> This e-mail message is subject to http://www.hw.ac.uk/disclaim.htm
> __________________________________________________________________
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
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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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-------------- next part --------------
#define _FF_GROMACS
#define _FF_GROMACS1
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 1 no 1.0 1.0
[ atomtypes ]
;name mass charge ptype c6 c12
CH3 15.03500 0.000 A 0.88765E-02 0.26150E-04
CH2 14.02700 0.000 A 0.90975E-02 0.35333E-04
OW 15.99940 0.000 A 0.26171E-02 0.26331E-05 1 2 3
HW 1.00800 0.000 A 0.00000E+00 0.00000E+00 4 5 6
[ bondtypes ]
CH2 CH2 1 0.15300 334720.
CH3 CH2 1 0.15300 334720.
[ angletypes ]
; i j k func th0 cth
CH3 CH2 CH2 1 111.000 460.240
CH2 CH2 CH2 1 111.000 460.240
[ dihedraltypes ]
CH2 CH2 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495
[ moleculetype ]
; Name nrexcl
C10 3
[ atoms ]
; nr type resnr residu atom cgnr charge
1 CH3 1 C10 C1 1 0.0
2 CH2 1 C10 C2 2 0.0
3 CH2 1 C10 C3 3 0.0
4 CH2 1 C10 C4 4 0.0
5 CH2 1 C10 C5 5 0.0
6 CH2 1 C10 C6 6 0.0
7 CH2 1 C10 C7 7 0.0
8 CH2 1 C10 C8 8 0.0
9 CH2 1 C10 C9 9 0.0
10 CH3 1 C10 C10 10 0.0
[ bonds ]
; i j
1 2
2 3
3 4
4 5
5 6
6 7
7 8
8 9
9 10
[ angles ]
; i j k
1 2 3
2 3 4
3 4 5
4 5 6
5 6 7
6 7 8
7 8 9
8 9 10
[ dihedrals ]
; i j k l type
1 2 3 4 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495 0 0 0 0 0 0
2 3 4 5 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495 0 0 0 0 0 0
3 4 5 6 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495 0 0 0 0 0 0
4 5 6 7 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495 0 0 0 0 0 0
5 6 7 8 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495 0 0 0 0 0 0
6 7 8 9 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495 0 0 0 0 0 0
7 8 9 10 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495 0 0 0 0 0 0
#ifdef FLEX_SPC
#include "flexspc.itp"
#else
#include "spc.itp"
#endif
[ system ]
Olie op de Golven
[ molecules ]
C10 50
SOL 389
#ifdef BIG
C10 50
SOL 389
C10 50
SOL 389
C10 50
SOL 389
#endif
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