[gmx-users] error
David van der Spoel
spoel at xray.bmc.uu.se
Mon Sep 6 19:21:36 CEST 2004
On Mon, 6 Sep 2004, Dinesh Pinisetty wrote:
>if you get this message it means you are doing MD, not EM.
>Set algorithm = steep
>in your mdp file.
algorithm is not in the mdp file you sent me.
>
>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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>
>--
>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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>_______________________________________________
>gmx-users mailing list
>gmx-users at gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-users
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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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