[gmx-users] reflecting boundary conditions wall

Hi dear gmx-users and developers, I'm working on a system involved with solid surface and solution, which using periodic boundary conditions in x and y directions only. I need to creat a virtual wall at both z=0 and z=z, but it should be a reflecting boundary conditions wall. It's like this: pr

[gmx-users] Implicit solvent problems

Hi, dear all, I’m doing the simulation involved in protein and some surface. I encounter this problem when trying to use implicit solvent model with GMX4.5.3. First, minimize. When doing this I got the result as below: Step= 0, Dmax= 1.0e-02 nm, Epot= -1.91727e+06 Fmax= 6.19542e+06, atom=

[gmx-users] Re: Implicit solvent problems

Dear all, Thank you for giving me some hints for my problems. The problems has been solved now, the key is to adjust the gb_dielectric_offset to a smaller value like 0.05， then theminimizationgets going normally. Subsequently, the NVT goes well. Still, I don’t quite understand what role theg