[gmx-users] error
David van der Spoel
spoel at xray.bmc.uu.se
Mon Sep 6 19:55:35 CEST 2004
On Mon, 6 Sep 2004, Dinesh Pinisetty wrote:
>
>
>
>
>Hi Dr.David,
> I tried using
> algorithm = steep.
> It still did not work for me
you need to checkout the online manual
I was wrong, there is no option algorithm
>The error reamins the same Only that The pressure scaling mu: values
>changed.
>Even i decreased tau_p to 1.0 1.0 from 2.0 2.0 it did not work for me.
>What else might be wrong Dr.david here.
>Thanking you,
>Dinesh.
>
>
>From:gmx-users-bounces at gromacs.org on 09/06/2004 07:21 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
>
>
>
>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.
>>> >>
>>> >>
>>> >> _______________________________________________
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>>> >> gmx-users at gromacs.org
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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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>
>--
>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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