[gmx-users] error

[Itamar Kass]

   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 6.90978e+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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