Dear All,
By gromacs pdb2gmx, we can choose the amber force field. Suppose we have chosen the amber force field, now let us see add ions.
By gromacs command "genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -neutral -conc 0.1", besides neutralize the system, we also add 0.1 mol/L NaCl to the system.
For AMBER, the comand to neutralize the system is as following: addions dna1(or some other name of the system) Na+ 0 or addions dna1 Cl- 0
>From my knowledge, in AMBER there is no command to add a certainm concentration of NaCl to the syste. But in its mdin file of the AMBER, we can specify "saltcon=0.1", which means salt concentration is 0.1 mol/L. As I have not tried, my current knowledge is that there would be no 0.1 mol/L NaCl added to the system by AMBER, but it will calculate as if there is 0.1 mol/L NaCl.
Then may I ask, for using AMBER force field by GROMACS, besides we add 0.1 mol/L NaCl by the command "genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -neutral -conc 0.1", shoud we also insert "saltcon=0.1" in the gromacs mdp file?
I am looking forward to getting a clarification from you.
Cheers,
Acoot
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Received on Sat Apr 21 2012 - 04:30:03 PDT
