[gmx-users] mdrun error

Dear users I got this error in my mdrun There is no domain decomposition for 4 nodes that are compatible with the given box and a minimum cell size of 7.1147 nm. my system contains graphene and surfactants. In last box I put graphene in the middle of my box and the graphene was npbc and the mdrun

[gmx-users] genion problem

Dear all I want to use bromide for neutralize my system. I wrote genion -s ions.tpr -c file.gro -p topol.top -pname K -nname BR -nn 24. After I cheked it the gromacs read Boron intead of bromide. I wrote command -nname BR -nn 24. and I did not use K but in all cases my output was boron and I did

[gmx-users] freezing graphene sheet

Dear all, I have simuated graphene and surfactants for 10 ns. When I visualized it by VMD, I saw that my graphene sheet was deformed. I put graphene finite. I am trying to freeze graphene sheet but I am not sure about the my mdp file. It would be really nice that someone tell me about freezing

[gmx-users] interval simulation

Dear all, I have run my input for 5 ns and now I want to extend it for another 5ns. I used some commands in the gromacs manual but it starts at first step again. the explanation in manual makes me confused. it would be realy helpful that someone tell me how can I use my output of mdrun as input