[gmx-users] error

[Dinesh Pinisetty]

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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