[gmx-users] error
Dinesh Pinisetty
dpinis1 at lsu.edu
Tue Sep 7 18:42:19 CEST 2004
Hello everybody,
When I tried to energy minimization using "integrator=steep" and
coloumbtype=PME
I was getting step=7192 Dmax=1.1e-06 nm Epot=-1.02807e+05 Fmax=1.18982e+02
atom=2065
But I have given number of steps to be 25,000 for Energy Minimization.It
did run for 7192 steps after that it displayed error as follows:
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax<10
Double precision normally gives you accuracy.
writing lowest energy coordinates.
Steepest Descents converged to machine precision in 7193 steps,but did not
reach requested Fmax<10.
Potential energy = -1.0280727e+05
Maximum force = 1.2036946e+02 on atom 2065
Norm of force = 5.1022946e+02
Here the atom coloumn also remained the smae 2065 why is it so,and how to
perform minimization till 25,000 steps.
Please help me out in minimizing the system to the desired values.Usually
what would be the values of Epotential etc in the case of DPPC membrane for
starting MD and how can here it can be achieved by avoiding the
error............Any help would be greatly appreciated..................
Thanking you,
Dinesh.
From:gmx-users-bounces at gromacs.org on 09/07/2004 08:35 AM ZE8
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
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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>>>>>>
>>>>>
>>>>>
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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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