[gmx-users] Energy minimisation

[Justin A. Lemkul]

Quoting JMandumpal <jesbman at rediffmail.com>:

> Dear Gromacs users
>
> When I run Energy minimisation using the command,
>
> grompp -f em.mdp -p topol.top -c out.gro -o pr.tpr, I received the following
> error message.
>
> **********************************************************
>
>  processing coordinates...
> double-checking input for internal consistency...
> 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.
>
> -------------------------------------------------------
> Program grompp, VERSION 3.3.2
> Source code file: grompp.c, line: 1111
>
> Fatal error:
> There were 1 error(s) processing your input
> -------------------------------------------------------
> *******************************************************************
>
> MY BOX DIMENSION IS 20.1 * 20.1 * 20.1

Angstoms or nanometers?

>
> I CHANGED THE RLIST, FOR A LOWER VALUE: STILL THE MESSAGE IS SAME.

What was the initial value?  What did you change it to?  What are you trying to
do?  You need to provide explicit information to get a useful response.

>
> Note: I copied the .mdp file form the gromacs users list ( DECMEBER 2001)

What is in this .mdp file?  There are lots out there on the archive...

-Justin

>
> regards,
> Jestin Mandumpal
>
>
>
>
>



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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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