[gmx-users] error
Chng Choon Peng
cpchng at bii.a-star.edu.sg
Tue Sep 7 02:35:12 CEST 2004
Hi all,
I've checked that the option is called "integrator" and not "algorithm".
So, it's "integrator = steep" or "integrator = cg" for energy minization and
"integrator = md" for molecular dynamics simulations.
cheers,
Choon-Peng
On 9/7/04 1:55 AM, "David van der Spoel" <spoel at xray.bmc.uu.se> wrote:
> 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.
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> 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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>>
>> --
>> 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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