Thanks Francesco.
I think after we use genion to add certain concentrations of salt in GROMACS, even we have use the AMBER force field in the GROMACS, the GROMACS will not request us to have "saltcon=0.1" in its mdp file, am I right?
Cheers,
Acoot
________________________________
From: Francesco Oteri <francesco.oteri.gmail.com>
To: amber.ambermd.org
Sent: Saturday, 21 April 2012 9:31 PM
Subject: Re: [AMBER] using AMBER forcefield by GROMACS
Dear Acoot,
saltcon is supposed to be used in implicint solvent MD just to give an
idea of the salt atoms number. The same for gromacs.
To specifiy a saltconcentration in amber, you have to manually calculate
the number of ions to add.
Remind that the system has to be neutral.
In gromacs is easier because genion can perform such a calculation.
A trick is generating the pdb with gromacs and then using such a pdb to
have the AMBER topology.
Francesco
Il 21/04/2012 13:24, Acoot Brett ha scritto:
> 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 - 05:00:04 PDT
