Re: [gmx-users] Re: Energy minimization problem(1-4 interaction at distance 3.540 is larger than the 1-4 table size 1.000 nm)

Hai Tsjerk, David, Mark and others, Thank you for all your responses. I had been successful in setting up simulation and also in understanding what David and Mark told. As Dr. David suggested, I started EM for single surfactant in vaccum and succes

Re: [gmx-users] Re: Energy minimization problem(1-4 interaction at distance 3.540 is larger than the 1-4 table size 1.000 nm)

Arun kumar wrote: Hi Tsjerk and others, I tried to simulate one surfactant and one chloride ion in 500 waters and got similar type of errors. I mean my system got collapsed for l-bfgs minimization and for steepest descent the potential energy is a large number.(obviously some

Re: [gmx-users] Document about file input format to GROMACS program?

root wrote: Dear GROMACS user: We downloaded the AMBER-03* potential parameters files (ffamber_v3.3.1-doc.tar.gz) linked with the page http://folding.stanford.edu/ffamber/index.html#validation. We tried to simulate the Dickerson dodecamer using the 3.3.1 gromacs version. Our simulation crash wh