[gmx-users] Cut off problem

Anik Sen aniksen at csmcri.org
Mon May 7 06:55:29 CEST 2012

Dear Gromacs users,

I am using GROMACS 3.3.2. I have a problem in setting the cut off of my MD-run.
I want to see the interaction between some small atoms keeping them inside a periodic box without adding any solvent; i.e interaction between the atoms in the vacuum.
I have a total of 18-25 atoms in my system. The initial minimization was ok, but in case of the MD run, the job is failing after a few steps with the error,
Fatal error:
"One of the box vectors has become shorter than twice the cut off length or one of the box diagonal element has become smaller than cut off".
I have already changed the ‘d’ and ‘rlist’; rvdw’ and rcoulomb’ to a number of different values to overcome the problem, but the problem persists.
How can I overcome this problem.

Thanking you in advance
Anik Sen
Anik Sen
CSIR-Central Salt & Marine Chemicals Research Institute,
Gijubhai Badheka Marg.
Bhavnagar, Gujarat 364002
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