On 21/04/2012 9:23 PM, Acoot Brett wrote:
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.
No. That's like using the Russian word for a car mid-sentence in a
Japanese textbook on architecture. Look up the context in which saltcon
is used in AMBER and you will see that this makes no sense for an
explicit solvent simulation in AMBER, never mind in GROMACS.
Mark
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