[gmx-users] error

David van der Spoel spoel at xray.bmc.uu.se
Mon Sep 6 10:21:38 CEST 2004


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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> >>
> >
> >
> > _______________________________________________
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> > gmx-users at gromacs.org
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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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