[gmx-users] Minimization-single or double precision

Dear Gromacs users, I wanted to know whether it is correct doing minimization in double precision and rest all - pdb2gmx, editconf, genbox, grompp and mdrun itself in single precision. I had got convergence during energy minimization using double precision but not single precision (input

[gmx-users] Doubts regarding Simulation box

Dear Gromacs users, I am new to gromacs. I want to simulate a system (protein) with a dodecahedron box in order to minimize the time. rlist = rcolumb = 1.2nm; (PME) rvdw = 1.1nm; rvdw_switch = 0 (using vdwtype = switch) so when giving the simulation box, should i give the value of

Re: [gmx-users] Density of the box

Sir, I am using Gromacs 4.0.7 version. Does this problem exits in other older or newer versions? what is the density of water that spc216 adds? If it is a fixed density, then i encountered a problem - I tried using 1 water molecule as a system (instead of protein), in a cubic box with 0.8nm

[gmx-users] Density of the box

Dear Gromacs users, I was trying to run a simulation using a protein of 123 aa long and wanted to adjust the density to 993.04g/l so with the following command I ran the editconf: editconf -f conf.pdb -o box.pdb -bt cubic -d 0.8 -density 997.0479 Its output was as follows: