[gmx-users] question

Justin Lemkul jalemkul at vt.edu
Sat Dec 30 17:17:15 CET 2017



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; 
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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