[gmx-users] dmso and water

[Dinesh Pinisetty]

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.
   What might be the reason..........
Thanking you,
Dinesh.


m:gmx-users-bounces at gromacs.org on 10/06/2004 10:37 PM ZE2


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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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