<html><head></head><body bgcolor="#FFFFFF"><div>yes all cutoffs 0 and epsilon_rf 1 and nstlist 0 as well.<br><br>Toodle pip!</div><div><br>On Nov 30, 2011, at 8:39 PM, "Shi, Huilin" <<a href="mailto:huilshi@imail.iu.edu">huilshi@imail.iu.edu</a>> wrote:<br><br></div><div></div><blockquote type="cite"><div>
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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi,<br>
<br>
I would like to run a gas-phase protein simulation (with charge state of +8). <br>
I have read this paper : Biochemistry, 2007, 47, 933-945.<br>
<br>
In the method section of vaccum simulation, it is said<br>
"For the remaining parameters, the same settings were used as in the water simulations,
<br>
except that the periodic boundary conditions were turned off and no cutoffs whatsoever were used."<br>
<br>
I am confused about "no cutoffs whatsoever were used".<br>
Does that mean setting all the cutoffs to be zero?<br>
In the md.mdp file, can I use the following<br>
<br>
"; NEIGHBORSEARCHING PARAMETERS<br>
nstlist = 0<br>
ns-type = simple<br>
pbc = no<br>
rlist = 0<br>
<br>
; OPTIONS FOR ELECTROSTATICS AND VDW<br>
coulombtype = cut-off<br>
rcoulomb = 0<br>
epsilon_rf = 78<br>
epsilon_r = 1<br>
vdw-type = Cut-off<br>
rvdw = 0"<br>
<br>
Do I need to set rcoulomb/rvdw to zero or some other number?<br>
<br>
Thank you.<br>
<br>
<br>
Huilin</div>
</div></blockquote><blockquote type="cite"><div><span>-- </span><br><span>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a></span><br><span><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a></span><br><span>Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!</span><br><span>Please don't post (un)subscribe requests to the list. Use the </span><br><span>www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.</span><br><span>Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a></span></div></blockquote></body></html>