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 href="mailto: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;">
<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="font-family: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; font-size: inherit; line-height: inherit; font-size-adjust: inherit; font-stretch: inherit;" valign="top">
<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>
</td></tr></tbody></table><br><br>--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote></div><br>