[gmx-users] error

[Dinesh Pinisetty]

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

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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