[gmx-users] dmso and water

[Dinesh Pinisetty]

Hi andre,
         I have increased the box vector in z direction as you told.I have
increased even in x and y directions.The highest value of in z direction
was 11.--- and highest value in x-direction and y direction was 6.---.I had
8 8 and 15 as my box vector lengths.Still the error remain the same.It did
not change.What can be the problem,by the way if you have any e-mail id can
I send the input files if you get time will u try with these and tell me
what the problem is.............
I will grateful to you if you can help me in this regard.
Thanking you,
Dinesh.


From:gmx-users-bounces at gromacs.org on 10/06/2004 06:32 PM GMT


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cc:   (bcc: Dinesh Pinisetty/dpinis1/LSU)

Subject:    Re: [gmx-users] dmso and water



On Wed, 6 Oct 2004, Dinesh Pinisetty wrote:

Hi Dinesh,

maybe the repulsive contacts take place between images, so you
would need to increase box length above/below the dmso and water
layers as well as between them. it should work, I've made it
already using three different layers and it worked just fine.

best regards,

andre'

>
>
>
>
> 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.
>


/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/

Dr. Andre' Farias de Moura

/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/

Laboratorio de Quimica Teorica
Universidade Federal de Sao Carlos
Sao Carlos - SP - Brasil

/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/

Endereco Atual

Grupo de Quimica Quantica
Instituto de Quimica de Sao Carlos
Universidade de Sao Paulo
Sao Carlos - SP - Brasil
Telefone: 55-16-3373-8055

/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/

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