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Berk,<br>
<br>
Thanks for the link to discussion related to the same topic. It was
really helpful in understanding the details of implementation and what
options are suitable.<br>
<br>
What I meant by shifting the potential was that the potential is
changed from the original form. From gromacs manual,<br>
<br>
"There is no fundamental difference between a switch function (which
multiplies the potential with<br>
a function) and a shift function (which adds a function to the force or
potential)"<br>
<br>
Thanks,<br>
Jeetain<br>
<br>
Berk Hess wrote:
<blockquote cite="mid:BLU134-W33C261523260B94BC2BA068E850@phx.gbl"
type="cite">
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<div style="text-align: left;">Hi,<br>
<br>
PME-switch does not shift, it only switches.<br>
It does not make sense to use plain PME with a cut-off,<br>
but also this in impossible with the way the Gromacs innerloops work.<br>
For a detailed (and long) discussion on this topic see:<br>
<a class="moz-txt-link-freetext" href="http://bugzilla.gromacs.org/show_bug.cgi?id=196">http://bugzilla.gromacs.org/show_bug.cgi?id=196</a><br>
</div>
<br>
Berk.<br>
<br>
<br>
<hr id="EC_stopSpelling">From: <a class="moz-txt-link-abbreviated" href="mailto:jeetain@gmail.com">jeetain@gmail.com</a><br>
To: <a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Date: Mon, 21 Jul 2008 16:00:26 -0400<br>
Subject: [gmx-users] How to modify code so that rlist > rcoulomb<br>
<br>
Hi Berk,
<div><br>
</div>
<div>Thanks for your response. I am trying to simulate the following
options,</div>
<div><br>
</div>
<div>
<div>ns_type = grid</div>
<div>rlist = 3.2</div>
<div>coulombtype = pme</div>
<div>rcoulomb = 1.0</div>
<div>vdw-type = cut-off</div>
<div>rvdw = 3.0</div>
<div>fourierspacing = 0.12</div>
<div>pme_order = 4</div>
<div>ewald_rtol = 1e-5</div>
<div>optimize_fft = yes</div>
<div><br>
</div>
<div>I tried the following with gromacs 3.3.99_development_200800503,</div>
<div><br>
</div>
<div>
<div>ns_type = grid</div>
<div>rlist = 3.2</div>
<div>coulombtype = pme-switch</div>
<div>rcoulomb = 1.0</div>
<div>rcoulomb_switch = 0.0</div>
<div>vdw-type = shift</div>
<div>rvdw = 3.0</div>
<div>rvdw_switch = 0.0</div>
<div>fourierspacing = 0.12</div>
<div>pme_order = 4</div>
<div>ewald_rtol = 1e-5</div>
<div>optimize_fft = yes</div>
<div><br>
</div>
</div>
<div>and it works. I want something similar to PME-Switch (rlist >
rcoulomb) but without shifting the real space coulomb part. Is this
possible? When I try the option rcoulomb_switch > rcoulomb, it gives
an error.</div>
<div><br>
</div>
<div>Thanks,</div>
<div>Jeetain</div>
</div>
<div><br>
</div>
<div><span class="EC_Apple-style-span"
style="font-family: Times; font-size: 16px;">
<pre>> Hi,
> You did not specify for which type of vdw and electrostatics you want this option.
> For plain cut-off's it does not make sense.
> In version 3.3 you can do what you want with the shift and switch options.
>
> In the CVS version there are also Reaction-Field-zero and PME-Switch.
>
> Berk.
><i> From: <a moz-do-not-send="true"
href="http://www.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">jeetain at gmail.com</a>
</i>><i> To: <a moz-do-not-send="true"
href="http://www.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">gmx-users at gromacs.org</a>
</i>><i> Date: Sat, 19 Jul 2008 16:38:59 -0400
</i>><i> Subject: [gmx-users] How to modify code so that rlist > rcoulomb
</i>><i>
</i>><i> Hi All,
</i>><i>
</i>><i> I want to simulate a system for which rvdw > rcoulomb and to account
</i>><i> for LJ interactions correctly rlist should be greater than rvdw (if
</i>><i> nstist != 1). For current gromacs setup rlist should be equal to
</i>><i> rcoulomb. I searched the mailing list and there has been several
</i>><i> discussions related to this issue such as,
</i>><i>
</i>><i> <a moz-do-not-send="true"
href="http://www.gromacs.org/pipermail/gmx-users/2006-July/022804.html"
target="_blank">http://www.gromacs.org/pipermail/gmx-users/2006-July/022804.html</a>
</i>><i>
</i>><i> I was wondering if anyone has implemented something already so that a
</i>><i> system with, rlist > rvdw > rcoulomb, can be simulated without any
</i>><i> problem. Can anyone please guide me what files / variables should be
</i>><i> changed to implement this.
</i>><i>
</i>><i> Thanks,
</i>><i> Jeetain
</i>><i> _______________________________________________
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