[gmx-users] md-error

[Dinesh Pinisetty]

Dear Dr.David,
        As you told again I restarted the MD simulation of the system with
96 DPPC molecules and water changing the input parameter rvdw to 1.4 and
having pressure coupling constant to only one value i.e 2.0 as I have
isotropic scaling,this time it run only for 5703 steps though I have it to
undergo 2000000 steps having step size of 0.002.

  When I check my md.log file it says that Water molecule starting at atom
(some number) cannot be settled.Check for bad contacts and/or reduce the
time step.

  Where the problem might be now........

The first time when it failed for rvdw=1.0 and haveing two pressure
coupling constants,it did run till 1,66,600 steps and there when I checked
md.log file the potential enrgy and total where nan,I think that might be
the problem there,how to sort out that problem.........

Please let how to avoid these errors and run the simulation...............
Thanking you,
Dinesh...





From:gmx-users-bounces at gromacs.org on 09/27/2004 08:24 AM ZE2


Sent by: gmx-users-bounces 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] md-error



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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