[gmx-users] genbox solvent addition inhomogeneous?
pim.frederix at strath.ac.uk
Fri Oct 15 17:22:08 CEST 2010
When I'm trying to create my solve box of 12x12x12 nm I encounter some trouble. I'm using Gromacs 4.5 with the MARTINI force field to set up a system of 400 dipeptide molecules in water. However when I use "genbox -cp <coarse grained dipeptidebox> -cs <MARTINI example water box> -vdwd 0.2 -o <output>" I get an inhomogeneous distribution of the water beads: there is what looks like a cubic higher density water box in the middle ~9 nm of the output. When I then try to run a energy minimization with mdrun the simulation crashes quickly with
Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 100.
Potential Energy = 7.8217890e+17
Maximum force = inf on atom 6750
Norm of force = inf
I've tried different vdwd's, using define = -DPOSRES, but I can't get round it. Using smaller 9x9x9 boxes with 150 dipeptides and further nothing different does work very satisfactory, but to study the assembled structure I would like to increase the size of the entire system.
Can anyone explain why this happens or suggest any solutions? Thanks very much,
PhD student University of Strathclyde
Pure & Applied Chemistry / Biomolecular & Chemical Physics
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