[gmx-users] question

[RAHUL SURESH]

On Sat, 30 Dec 2017 at 9:47 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/30/17 1:39 AM, s.ghasemlou wrote:
> > Hello every one,
> >
> > After using the command "g_grompp -f em.mdp -c totalbox1.gro -p
> > topol.top -o ions.tpr" I get the error:
> >
> > ERROR 1 [file topol.top, line 863]:
> >    ERROR: The cut-off length is longer than half the shortest box vector
> > or
> >    longer than the smallest box diagonal element. Increase the box size
> > or
> >    decrease rlist.(my box vectors are 31.16343- 31.16343- 31.16343)
>
> Check to be sure; it seems impossible to me that conventional cutoffs
> could trigger such an error with such a large box. Make sure that you're
> not thinking in A and trying to use nm (GROMACS convention).
>
> > I have tried different rlist, r columb and rvdw values. I have also
> > changed the box vector several times, but I still get the same error. I
> > don't know how to change them to fix the error.
> >
> > There is also the below warning:
> >
> > Warning: atom name 1 in topol.top and totalbox1.gro does not match (H55
> > - OW)
> > Warning: atom name 2 in topol.top and totalbox1.gro does not match (C2 -
> > HW1)
> > Warning: atom name 3 in topol.top and totalbox1.gro does not match (H53
> > - HW2)
> > Warning: atom name 4 in topol.top and totalbox1.gro does not match (H54
> > - OW)
> > Warning: atom name 5 in topol.top and totalbox1.gro does not match (C1 -
> > HW1)
> > Warning: atom name 6 in topol.top and totalbox1.gro does not match (H51
> > - HW2)
> > Warning: atom name 7 in topol.top and totalbox1.gro does not match (H52
> > - OW)
> > Warning: atom name 8 in topol.top and totalbox1.gro does not match (C50
> > - HW1)
> > Warning: atom name 9 in topol.top and totalbox1.gro does not match (H109
> > - HW2)
> > Warning: atom name 10 in topol.top and totalbox1.gro does not match
> > (H110 - OW)
> > Warning: atom name 11 in topol.top and totalbox1.gro does not match (O43
> > - HW1)
> > Warning: atom name 12 in topol.top and totalbox1.gro does not match (C42
> > - HW2)
> > Warning: atom name 13 in topol.top and totalbox1.gro does not match (C44
> > - OW)
> > Warning: atom name 14 in topol.top and totalbox1.gro does not match (C40
> > - HW1)
> > Warning: atom name 15 in topol.top and totalbox1.gro does not match (C41
> > - HW2)
> > Warning: atom name 16 in topol.top and totalbox1.gro does not match
> > (H100 - OW)
> > Warning: atom name 17 in topol.top and totalbox1.gro does not match (C46
> > - HW1)
> > Warning: atom name 18 in topol.top and totalbox1.gro does not match
> > (H102 - HW2)
> > Warning: atom name 19 in topol.top and totalbox1.gro does not match (C45
> > - OW)
> > Warning: atom name 20 in topol.top and totalbox1.gro does not match
> > (H101 - HW1)
>
> Your topology is out of order with respect to the coordinates. The order
> of the [molecules] section in your .top must be identical to the order
> of the appearance of coordinates. This is not the case in your system,
> so you need to correct it. Do not use -maxwarn under any circumstances;


Dear Justin

1. For The above mentioned error is it advisable to manually edit the gro
file or top file?

2. What will the situation to use the flag “-maxwarn” ?


> you will get a physically invalid system.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*