[gmx-users] md-error

[David]

On Mon, 2004-09-27 at 04:52, Dinesh Pinisetty wrote:
> 
> 
> Dear Dr.David,
>            I have taken the .mdp file from Dr.Tielmann's website and did
> work fine for 64 DPPC molecules on a monolayer and with water around.
>     I did not get your question "why do you have two pressure coupling
> constants? What is the third?" what do you mean by this.Please clarify this
> to me and suggest what to be modified and how?
check the online manual. either you specify one constant for isotropic
scaling or more than one for anisotropic. check you r md.log file for
the value of the resulting constants.

> You also asked me to change rvdw,the value I have now is 1.0 is 1.4 enough
> or should it be more. Can I start the simulation from the point it got
> crashed if yes how to do that?
if this is meant as equilibration then yes. for production you can not
defend changing the cut-off halfway the simulation.

> I will grateful to you if you could answer me these questions.
> Thanking you,
> Yours sincerely,
> Dinesh.
> 
> 
> 
> From:gmx-users-bounces at gromacs.org on 09/26/2004 10:45 AM ZE2
> 
> 
> Sent by: gmx-users-bounces at gromacs.org
> 
> Please respond to Discussion list for GROMACS users <gmx-users at gromacs.org>
> 
> 
> 
> To:   Discussion list for GROMACS users <gmx-users at gromacs.org>
> cc:   (bcc: Dinesh Pinisetty/dpinis1/LSU)
> 
> Subject:    Re: [gmx-users] md-error
> 
> 
> 
> On Sun, 2004-09-26 at 03:26, Dinesh Pinisetty wrote:
> >
> >
> > Hello everybody,
> >        When I started of MD simulation of DPPC bilayer(96 molecules on
> each
> > monolayer) and water on either side of the monolayer for 4ns i.e. 2000000
> > steps. It did run till step 166600 and then shows error as Segmentation
> > fault and stopped.The Warnings are as follows:
> >
> > Warning: 1-4 interactions between 6501 and 6506 at distance larger than
> 2nm
> > turn on -debug for more information
> >
> > Step 166599  Warning: pressure scaling more than 1%, mu: 1.01263
> 1.01263
> > 1.01263
> >
> > Step 166600  Warning: pressure scaling more than 1%, mu: 1.07707 1.07707
> > 1.07707
> > Wrote pdb files with previous and current coordinates
> > Segmentation fault
> >
> > This is the error it has shown.What might be the mistake and how to sort
> it
> > out.
> >  I have viewed the .xtc file till step 166600 it was fine,but
> unfortunately
> > it crashed.If I sort the mistake by anyones suggestion can I continue
> from
> > the point it had crashed,if so how to do it.
> > Any suggestions would be greatly helpful to me.
> > By the way my .mdp file is attached to this mail.Please check this out
> once
> > so that mistake can be identified by any of you.
> 
> 
> Check the box dimensions during the simulation (using g_energy). You may
> need to have a large VDW cut-off because the lipid head (charge) groups
> are very large.
> 
> > I hopw you will do the needful.
> > Thanking 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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