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On 21/04/2012 9:23 PM, Acoot Brett wrote:
<blockquote
cite="mid:1335007393.7235.YahooMailNeo@web121803.mail.ne1.yahoo.com"
type="cite">
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helvetica, sans-serif;font-size:12pt">
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<font face="times new roman, new york, times, serif">Dear All,</font></div>
<div> </div>
<div><font face="times new roman, new york, times, serif">By
gromacs pdb2gmx, we can choose the amber force field.
Suppose we have chosen the amber force field, now let us see
add ions.</font></div>
<div> </div>
<div><font face="times new roman, new york, times, serif">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.</font></div>
<div> </div>
<div><font face="times new roman, new york, times, serif">For
AMBER, the comand to neutralize the system is as following:
<font>addions dna1(or some other name of the system) Na+ 0
or addions dna1 Cl- 0</font></font></div>
<div> </div>
<div><font face="times new roman, new york, times, serif">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 "<b><font>saltcon=0.1</font></b>",
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.</font></div>
<div> </div>
<div><font face="times new roman, new york, times, serif">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 "<b><font>saltcon=0.1</font></b>"
in the gromacs mdp file?</font></div>
<div> </div>
<div><font face="times new roman, new york, times, serif">I am
looking forward to getting a clarification from you.</font></div>
</div>
</blockquote>
<br>
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.<br>
<br>
Mark<br>
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