[gmx-users] dmso and water

[David van der Spoel]

On Wed, 2004-10-06 at 23:05, Dinesh Pinisetty wrote:
> 
> 
> Hello Dr.David,
>         I increased the gap between them and tried again but no use it
> shows the same error.After attaching the pdb part of DMSO to water and
> after creating a new pdb file with both.I am translating the whole system
> by 1 in z direction and then trying to perform energyminimization,but it
> shows the same error.
Take this conformation and make the box 10 x 10 x 10.

>    What might be the reason..........
> Thanking you,
> Dinesh.
> 
> 
> m:gmx-users-bounces at gromacs.org on 10/06/2004 10:37 PM ZE2
> 
> 
> Sent by: gmx-users-bounces at gromacs.org
> 
> Please respond to Discussion list for GROMACS users <gmx-users at gromacs.org>
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> 
> 
> To:   Discussion list for GROMACS users <gmx-users at gromacs.org>
> cc:   (bcc: Dinesh Pinisetty/dpinis1/LSU)
> 
> Subject:    Re: [gmx-users] dmso and water
> 
> 
> 
> On Wed, 2004-10-06 at 22:22, Dinesh Pinisetty wrote:
> >
> >
> > Hello all,
> >       Is it possible to cause mixing of DMSO and water.
> > I have 2713 water molecules in a simulation box and 548 molecules of DMSO
> > in a seperate one.I arranged one over them with a very small gap between
> > them.Now when I am trying to energy minimize the system I am getting
> error
> > as follows:
> >
> make the gap bigger than a DMSO molecule.
> > FATAL error: ci = -2147483648 should be in 0 .. 4393 [FILE nsgrid.c, LINE
> > 218]
> >
> > Could anyone guess what the reason might be,is it that DMSO and WATER
> > cannot mix with each other.I have checked the box size,all the three
> > co-ordinates of the box size are greater than the max values of x,y,z
> > co-ordinates of all the atoms present in the system.
> >  What might be the mistake if this error occurs other then box size.
> >  I am grateful to any help extended in this regard.........
> > Thank you,
> > Dinesh.
> >
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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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-- 
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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