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 Student CSIR-Central Salt & Marine Chemicals Research Institute, Gijubhai Badheka Marg. Bhavnagar, Gujarat 364002 [www.csmcri.org] ========================================================
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