[gmx-users] Parameterisation of transition metal ions in gromacs

Hi, I have to do simulations in GROMACS with Vanadium ions (V+3,V+2,VO2+) but non bonded parameters for vanadium are not present in gromos forcefield. Can anyone please let me know how can I find parameters for vanadium or if anyone has found these parameters in literature? Also I tried to find

[gmx-users] Potential for Frozen atoms

Hi, I wanted to find out site-site potential between two Copper(Cu+2) ions at a particular distance and fixed geometry. So I constructed a box containing 2 Cu+2 and 2 sulfate ions very far away to make the system charge zero. Then i froze these atoms and did energy minimization step. But in result

Re: [gmx-users] Potential for Frozen atoms

mdp file: ; VARIOUS PREPROCESSING OPTIONS title= cpp = /lib/cpp include = define = -DPOSRES ; RUN CONTROL PARAMETERS integrator = l_bfgs ; Start time and timestep in ps tinit= 0 dt

Re: [gmx-users] Potential for Frozen atoms

Actually I just want to find out potential between two Cu2+ ions, but as gromacs doesn't allow total charge to be a non zero value, I had to add two sulphate ions. So I kept 2 sulphate ions at a distance more than cutoff distance from each copper ion as well as from each other. Regards Sukriti --

[gmx-users] System coordinates not getting freezed

Hi everyone, My system contains one copper ion and one water molecule with no solvent. I considered complete system as one group and freezed the system. But the coordinates are not getting fixed. Also when i took the same mdp file with 2 copper ions instead of one cu and one water, the system was