<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Thanks a lot for your help guys, I think I found it.<br><br>Best Regards, Chrysostomos<br><br>--- Στις <b>Πέμ., 01/07/10, ο/η Gaurav Goel <i><gauravgoeluta@gmail.com></i></b> έγραψε:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>Από: Gaurav Goel <gauravgoeluta@gmail.com><br>Θέμα: Re: [gmx-users] Problem with Lennard Jones cross terms<br>Προς: "Discussion list for GROMACS users" <gmx-users@gromacs.org><br>Ημερομηνία: Πέμπτη, 1 Ιούλιος 2010, 18:16<br><br><div id="yiv465261369"><br><br><div class="gmail_quote">2010/7/1 xrysostomos sfhsdfghsdfhsdgh <span dir="ltr"><<a rel="nofollow" ymailto="mailto:cbatiss@yahoo.gr" target="_blank" href="/mc/compose?to=cbatiss@yahoo.gr">cbatiss@yahoo.gr</a>></span><br><blockquote class="gmail_quote"
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Dear Gaurav<br><br>Thanks a lot for your quick reply<br><br>I have done also what you suggested but the result is the same. I mean that I observe stronger adsorption of the polymers to the surface, when I increased the values of c6 and c12 for Si in the<span style="font-weight: bold;"> [atomtypes]</span>, but continue having original values in the <b>[ nonbond_params ].</b> <br>
But in general, am I not able with gromacs to switch-off the LJ interactions between the polymers and the substrate?<br>Is it possible to have this problems because I use NVT ensemble?<br></td></tr></tbody></table></blockquote>
<div><br>You can switch-off all non-bonded interactions between a pair of energy groups by defining Energy group exclusions. Sec. 7.3.19 of the gromacs manual 4.0.<br><br>-Gaurav<br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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<br>Thanks again, Chrysostomos<br>--- Στις <b>Πέμ., 01/07/10, ο/η Gaurav Goel <i><<a rel="nofollow" ymailto="mailto:gauravgoeluta@gmail.com" target="_blank" href="/mc/compose?to=gauravgoeluta@gmail.com">gauravgoeluta@gmail.com</a>></i></b> έγραψε:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;">
<br>Από: Gaurav Goel
<<a rel="nofollow" ymailto="mailto:gauravgoeluta@gmail.com" target="_blank" href="/mc/compose?to=gauravgoeluta@gmail.com">gauravgoeluta@gmail.com</a>><br>Θέμα: Re: [gmx-users] Problem with Lennard Jones cross terms<br>Προς: "Discussion list for GROMACS users" <<a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Ημερομηνία: Πέμπτη, 1 Ιούλιος 2010, 16:10<div><div></div><div class="h5"><br><br><div>By specifying both c6 and c12 to be zero, you've set both the attractive and repulsive components of SI-OA, Si-CH2, Si-CH3 dispersion interactions to zero. If you don't have any electrostatic repulsions in your system polymer might be "attracted" to Silica substrate for entropic reasons...e.g., centers of mass of Si and CH2 can overlap without any energy penalty.<br>
<br>One solution will be to fix c6, c12 for SI-OA, Si-CH2, Si-CH3 to their original values under <b>[ nonbond_params ] </b>and then do whatever you want to do with the Si-Si interactions in [atomtypes].<br><br>-Gaurav<br>
<br><div class="gmail_quote">2010/7/1 xrysostomos sfhsdfghsdfhsdgh <span dir="ltr"><<a rel="nofollow" target="_blank" href="http://mc/compose?to=cbatiss@yahoo.gr">cbatiss@yahoo.gr</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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<p class="MsoNormal" style="margin-bottom: 2pt; text-align: justify;">I am trying
to simulate the following system: 5-layer FCC substrate consisting of Si particles
which interact only with Lennard-Jones potential and vertical to the substrate
I put polymer chains of (CH2-OA), starting from a distance of 0,4nm. </p>
<p class="MsoNormal" style="margin-bottom: 2pt; text-align: justify;">What I want
is to be able to manage completely independently the LJ interactions between
the substrate and the polymers and not according to the combination rules, i.e.
to have very very strong LJ interaction only between the Si particles but these
to interact normally with the polymer chains.</p>
<p class="MsoNormal" style="margin-bottom: 2pt; text-align: justify;">I use the
Gromos-96 force-field. The initial values for the c6 and c12 parameters are the
following:</p>
<p class="MsoNormal" style="margin-bottom: 2pt; text-align: justify;"><b>[ atomtypes ]</b></p>
<p class="MsoNormal" style="margin-bottom: 2pt; text-align: justify;">name<span> </span>at.num<span>
</span>mass<span> </span>charge<span> </span>ptype<span>
</span><span> </span>c6<span> </span><span> </span>c12</p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: justify;">OA<span> </span><span> </span><span> </span><span> </span><span> </span><span> </span>8<span> </span><span> </span><span> </span><span> </span>0.000<span>
</span>0.000<span> </span>A<span> </span><span> </span><span> </span>0.0022619536<span>
</span><span> </span>1.505529e-06</p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: justify;">CH2<span> </span><span> </span><span> </span>6<span> </span><span> </span><span> </span><span> </span><span> </span>0.000<span>
</span>0.000<span> </span>A<span> </span><span> </span><span> </span>0.0074684164<span>
</span><span> </span>3.3965584e-05</p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: justify;">SI<span> </span><span> </span><span> </span>14<span> </span><span> </span>0.000<span> </span>0.000<span>
</span>A <span> </span><span> </span><span> </span>0.01473796<span> </span><span> </span>2.2193521e-05</p>
<p class="MsoNormal" style="text-align: justify;"> </p>
<p class="MsoNormal" style="margin-bottom: 6pt; text-align: justify;"><b>[ nonbond_params ]</b></p>
<p class="MsoNormal" style="margin-bottom: 6pt; text-align: justify;">i<span> </span><span> </span><span> </span>j<span> </span><span> </span>func<span>
</span>c6<span> </span><span> </span><span> </span>c12</p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: justify; line-height: normal;">SI<span>
</span>OA<span> </span><span> </span><span> </span>1 <span> </span><span> </span>0.0000000<span> </span><span> </span><span> </span>0.00000000</p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: justify; line-height: normal;">SI<span>
</span>CH2<span> </span><span> </span>1<span> </span><span> </span>0.0000000 <span> </span><span> </span>0.00000000</p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: justify; line-height: normal;">SI<span>
</span>CH3<span> </span><span> </span>1<span> </span><span> </span><span> </span>0.0000000
<span> </span><span> </span>0.00000000</p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: justify; line-height: normal;"> </p>
<p class="MsoNormal" style="margin-bottom: 2pt; text-align: justify; line-height: normal;">What I did is to run 2 different simulations in NVT ensemble. In the <i>first</i>, I multiplied by 10 the c6, c12
values of Si in the [atomtypes ] <span> </span>and in
the <i>second</i> I multiplied (the initial
values again) by 100. In both cases I didn’t change the values on the [nonbond_params
].</p>
<p class="MsoNormal" style="margin-bottom: 2pt; text-align: justify; line-height: normal;">I would expect that in both cases there should be no adsorption of the
polymers in the substrate, since I <span> </span>change the interaction between the substrate and
the polymers in the [nonbond_params ] equal to zero.</p>
<p class="MsoNormal" style="margin-bottom: 2pt; text-align: justify; line-height: normal;">What I observed is that after 50000 steps with 2 fs time step the
polymers in the second case adsorbed to the surface.</p>
<p class="MsoNormal" style="margin-bottom: 2pt; text-align: justify; line-height: normal;">Can anybody help me or explain me why is this happening?</p>
<p class="MsoNormal" style="margin-bottom: 2pt; text-align: justify; line-height: normal;"> </p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: justify; line-height: normal;">Thanks in advance</p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: justify; line-height: normal;"> </p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: justify; line-height: normal;">Chrysostomos</p>
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