[gmx-users] error
Dinesh Pinisetty
dpinis1 at lsu.edu
Mon Sep 6 19:14:23 CEST 2004
Hi Dr.David,
I am sending you my .mdp file.Please check this out once.Its the
same .mdp file which I used to perform Energy Minimization on the DPPC
membrane system downloaded from Dr.Tielmenn's website.It did work fine
then,so i thought of using the same file again.
After performing grompp I am getting .tpr file.Then again if try EM by
mdrun -nice 0 -v -s input.tpr -o m.trr -c m.gro -e m.edr .I am getting the
error as
step 0
> Step 1 Warning: pressure scaling more than 1%, mu: 1.03558 1.03558
1.03558
> Segmentation fault
Now please check this file and help me out..........
Thanking you,
Dinesh.
From:gmx-users-bounces at gromacs.org on 09/06/2004 10:21 AM ZE2
Sent by: gmx-users-bounces at gromacs.org
Please respond to Discussion list for GROMACS users <gmx-users at gromacs.org>
To: gmx-users at gromacs.org
cc: (bcc: Dinesh Pinisetty/dpinis1/LSU)
Subject: Re: [gmx-users] error
On Mon, 2004-09-06 at 00:11, Dinesh Pinisetty wrote:
>
>
> Hi,
> I sorted out the problem of warning between the atoms.I am using
berendsen
> pressure coupling.Now that when i am trying to do Energy Minimization I
get
> an error as follows:
> step 0
> Step 1 Warning: pressure scaling more than 1%, mu: 1.03558 1.03558
1.03558
> Segmentation fault
if you get this message it means you are doing MD, not EM.
Set algorithm = steep
in your mdp file.
If you intended to do MD, increase tau_p.
>
> I am getting the above error.What does this mean,how to sort this
pressure
> scaling problem,and where might be the mistake for this segmentation
> fault.......
> I hope you will do the needful.Thanks a lot.
> Dinesh....
>
>
>
> From:gmx-users-bounces at gromacs.org on 09/05/2004 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>
>
>
>
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> cc: (bcc: Dinesh Pinisetty/dpinis1/LSU)
>
> Subject: Re: [gmx-users] error
>
>
>
> When you do the EM the program state which Atom make the problem (if the
> EM starts). If not try to look at defects at the beginning structure.
> Like
> "Step0Warning: 1-4 interaction between 2401 and 2406 at distance
larger..."
> means there is a problem at that location, try looking at bonds length,
> angles and distances between atoms.
> More over, try to use rvdw = rlist = rcouloumb.
> BTW what is your pressure coupling algorithm? If you use
> Parrinello-Rahman
> try use Berendsen.
>
> Have a nice trying, Itamar.
>
>
> ----- Original Message -----
> From: "Dinesh Pinisetty" <dpinis1 at lsu.edu>
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Sent: Sunday, September 05, 2004 9:11 PM
> Subject: Re: [gmx-users] error
>
>
> >
> >
> >
> >
> > Hi,
> > When I was trying to do Energy Minimization I got this error.What do
> you
> > mean by starting point defect,How to sort it out. Where might be the
> > mistake.............
> > Thanking you,
> > Dinesh.
> >
> > From:gmx-users-bounces at gromacs.org on 09/05/2004 08:56 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] error
> >
> >
> >
> > This is probably due to starting point which has some to defect, did
you
> > minimize the system first?
> >
> > ----- Original Message -----
> > From: "Dinesh Pinisetty" <dpinis1 at lsu.edu>
> > To: <gmx-users at gromacs.org>
> > Sent: Sunday, September 05, 2004 1:26 AM
> > Subject: [gmx-users] error
> >
> >
> >>
> >>
> >>
> >>
> >> hello all,
> >> Could anyone tell what this error means and how to sort out
> >> this.......
> >> Step0Warning: 1-4 interaction between 2401 and 2406 at distance
larger
> >> than
> >> 2.4nm.
> >> These are ignored for rest of the simulation turn on -debug for more
> >> information.
> >>
> >> Step1 Warning: pressure scaling more than 1%, mu: 6.90978e+18 6.90978
> e+18
> >> 6.90978e+18
> >>
> >> Warning: Only triclinic boxes with first vector parallel to the
x-axis
> > and
> >> the second vector in xy-plane are supported.
> >> Box(3*3)
> >> Box[ 0]={ nan, nan, nan}
> >> Box[ 1]={ nan, nan, nan}
> >> Box[ 2]={ nan, nan, nan}
> >> Can not fix pbc
> >>
> >> Warning: Only triclinic boxes with first vector parallel to the
x-axis
> > and
> >> the second vector in xy-plane are supported.
> >> Box(3*3)
> >> Box[ 0]={ nan, nan, nan}
> >> Box[ 1]={ nan, nan, nan}
> >> Box[ 2]={ nan, nan, nan}
> >> Can not fix pbc
> >>
> >> Warning: Only triclinic boxes with first vector parallel to the
x-axis
> > and
> >> the second vector in xy-plane are supported.
> >> Box(3*3)
> >> Box[ 0]={ nan, nan, nan}
> >> Box[ 1]={ nan, nan, nan}
> >> Box[ 2]={ nan, nan, nan}
> >> Can not fix pbc
> >>
> >> Warning: Only triclinic boxes with first vector parallel to the
x-axis
> > and
> >> the second vector in xy-plane are supported.
> >> Box(3*3)
> >> Box[ 0]={ nan, nan, nan}
> >> Box[ 1]={ nan, nan, nan}
> >> Box[ 2]={ nan, nan, nan}
> >> Can not fix pbc
> >>
> >> Warning: Only triclinic boxes with first vector parallel to the
x-axis
> > and
> >> the second vector in xy-plane are supported.
> >> Box(3*3)
> >> Box[ 0]={ nan, nan, nan}
> >> Box[ 1]={ nan, nan, nan}
> >> Box[ 2]={ nan, nan, nan}
> >> Can not fix pbc
> >>
> >> Warning: Only triclinic boxes with first vector parallel to the
x-axis
> > and
> >> the second vector in xy-plane are supported.
> >> Box(3*3)
> >> Box[ 0]={ nan, nan, nan}
> >> Box[ 1]={ nan, nan, nan}
> >> Box[ 2]={ nan, nan, nan}
> >> Can not fix pbc
> >>
> >> Warning: Only triclinic boxes with first vector parallel to the
x-axis
> > and
> >> the second vector in xy-plane are supported.
> >> Box(3*3)
> >> Box[ 0]={ nan, nan, nan}
> >> Box[ 1]={ nan, nan, nan}
> >> Box[ 2]={ nan, nan, nan}
> >> Can not fix pbc
> >>
> >> Warning: Only triclinic boxes with first vector parallel to the
x-axis
> > and
> >> the second vector in xy-plane are supported.
> >> Box(3*3)
> >> Box[ 0]={ nan, nan, nan}
> >> Box[ 1]={ nan, nan, nan}
> >> Box[ 2]={ nan, nan, nan}
> >> Can not fix pbc
> >>
> >> Fatal error: ci=-1 should be 0 .. -1.[FILE nsgrid.c LINE 218]
> >>
> >> What does the above error mean,How to sort it out.My .mdp file has
> >> rvdw=1.4,rlist=0.9,rcouloumb=0.9.I am using PME type.
> >>
> >> Please help me out in this regard.........
> >> Thanking you,
> >> Dinesh.
> >>
> >>
> >> _______________________________________________
> >> gmx-users mailing list
> >> gmx-users at gromacs.org
> >> http://www.gromacs.org/mailman/listinfo/gmx-users
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> >>
> >
> >
> > _______________________________________________
> > gmx-users mailing list
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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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