Example of a general input parameter files for Gromacs 4 for using flexDQ water model.
For the usage of Gromacs, please check http://www.gromacs.org/
md-xxx.mdp is the input parameter for mdrun
xxx.gro is the initial structure of the system
topol-xxx.top is the topology file
index-xxx.ndx is generated from make_ndx, grps name should be same with .mdp
-table gives the prefix of the tabulated potential files
Water .itp should be included in the .top file (#include flexdq.itp)
Here, we put all the input parameter files used in each files folder.
User can run a simulation directly in the certain directory.
###For DPPC membrane system:
grompp -f md-mem.mdp -c mem.gro -p topol-mem.top -n index-mem.ndx -o md.tpr
mdrun -deffnm md -table md (For DPPC-water system, the parameters of DPPC are from MARTINI force field. We combine DPPC parameters with our flexDQ parameters by optimization of SFE for each particle types given from MARTINI)
######### ###Other systems will be updated later... #########
###For Na system:
grompp -f md-na.mdp -c na.gro -p topol-na.top -n index-na.ndx -o md.tpr
mdrun -deffnm md -table md
###For Cl system:
grompp -f md-cl.mdp -c cl.gro -p topol-cl.top -n index-cl.ndx -o md.tpr
mdrun -deffnm md -table md
###For CH4 system:
grompp -f md-ch4.mdp -c ch4.gro -p topol-ch4.top -n index-ch4.ndx -o md.tpr
(For CH4 system, one first need to choose ./ch4-b/ or ./ch4-s/ to run.
Then rename the md_CH4_O-x.xvg to md_CH4_O.xvg, md_CH4_H-x.xvg to md_CH4_H.xvg.
So that we do not have to modified the parameters in .mdp or .ndx)
mdrun -deffnm md -table md