[gmx-users] Something wrong with the force field parameter

small molecular. But when I run the energy minimization for this molecular, the atoms detached and run out of the bond range. There must be something wrong with the force field parameter. Would you kindly show me, how to generate the force field parameter for the oplsaa? Thanks SUN,Jian

[gmx-users] pdb2gmx error, How to generate the gro and top file for a small molecular?

Dear all,   I am doing the simulation of a protein with a small molecular in its active site. But unfortunately, pdb2gmx cannot generate the gro and top file for the small molecualr? I am using the oplsaa force field, who can tell me how to generate the gro and top files?   Thanks a lot Jian __

gmx-users@gromacs.org

ful for newbies like me. :-) Thanks & Regards, Jian SUN, Jian wrote: Dear all, I am running simulated annealing for a protein in water and found something strange: 1. the poteintial energy keep on rising while the system is cooling down conservation of energy? 2. several LINCS WARNING

gmx-users@gromacs.org

Dear all, I am running simulated annealing for a protein in water and found something strange: 1. the poteintial energy keep on rising while the system is cooling down 2. several LINCS WARNINGs are given (I have posted the question but no reply till now) and then the energies become "nan" Who can

[gmx-users] LINCS WARNING "max 2022834176.000000 (between atoms 5655 and 5658) rms 81089176.000000"

Dear all, I am running the simulated annealing for a protein solvented in a water box, but I get such LINCS WARNING as "max 2022834176.00 (between atoms 5655 and 5658) rms 81089176.00" Why? Does it mean that my system is exploring? The following is my mdp file and some of the LINCS WARNI

[gmx-users] How to use the simulated annealing porotocal of gromacs 3.3?

Dear all, I am trying to use the simulated annealing porotocal of gromacs 3.3 (single precision) to find the global energy minimization of a protein in a water box. I set the mdp file as follow: ; VARIOUS PREPROCESSING OPTIONS title= Simul