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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi,<br>
<br>
Thank you for your reply.<br>
<br>
My concern is that if rcoulomb and rvdw are set to be zero, does it mean that <br>
there are no coulombic and van der waals forces involved in the simulation?<br>
<br>
I guess there are still coulombic and van der waals forces between atoms of a single protein molecule.<br>
<br>
Or does setting the cutoff to be zero just mean there is no forces between neighbored molecules?<br>
<br>
Thanks.<br>
<br>
<br>
Huilin<br>
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<div style="direction: ltr;" id="divRpF150028"><font color="#000000" face="Tahoma" size="2"><b>From:</b> gmx-users-bounces@gromacs.org [gmx-users-bounces@gromacs.org] on behalf of David van der Spoel [spoel@xray.bmc.uu.se]<br>
<b>Sent:</b> Wednesday, November 30, 2011 3:00 PM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> Re: [gmx-users] gas-phase protein simulation<br>
</font><br>
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<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" target="_blank">huilshi@imail.iu.edu</a>> wrote:<br>
<br>
</div>
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<div style="direction: ltr; font-family: Tahoma; color: rgb(0, 0, 0); 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>
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</blockquote>
<blockquote type="cite">
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