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Using two different potentials will cause all kinds of trouble, as
you will have jumps<br>
in the potential when a particle moves from one region to the other.<br>
If you want to do something like this you have to come up with a
potential<br>
which depends continuously on the distance and z-coordinates of the
two particles.<br>
You could implement this in the generic non-bonded kernel.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 03/28/2012 01:33 AM, Beste Bayramoglu wrote:
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Thanks for your response Anton!
<div><br>
</div>
<div>The reason that I want to use different potentials for the
same pairs in different regions is that because they are in
different environments when they are in different regions. I
cannot use the same potentials for all the environments they are
in, so that's why I should modify the code such that it assigns
a specific potential table for, let's say 0<box_z<2nm, and
then another one for the rest of the simulation box_z (for the
same energy group pair, of course). </div>
<div><br>
</div>
<div>Any comment from anyone is appreciated.</div>
<div><br>
</div>
<div>Thanks, </div>
<div><br>
</div>
<div>Beste<br>
<br>
<div class="gmail_quote">On Tue, Mar 27, 2012 at 5:05 AM, Anton
Feenstra <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:k.a.feenstra@vu.nl">k.a.feenstra@vu.nl</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im">On 27/03/12 10:30, Beste Bayramoglu wrote:<br>
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.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im">
Hi,<br>
<br>
I’ve been performing molecular dynamics simulations
using tabulated<br>
potentials with Gromacs version 4.0.7. Everything works
fine with one<br>
tabulated potential table for each type of energy group
pair. However,<br>
what I need to do now is that I need to use multiple
position-dependent<br>
nonbonded potentials (in tabulated form) for each of my
energy group<br>
</div>
pairs.That’s to say, for a certain energy group pair, I
need to assign
<div class="im"><br>
multiple tables and the program should decide on which
one to use in the<br>
calculations depending on the positions of the atoms
along z-direction.I<br>
was wondering if any unofficial attempts to modify the
source code have<br>
been made so far for a similar purpose. And which part
of the code<br>
should be changed? I checked the mail list archives, but
could not find<br>
such an entry. I know that this is going to be a very
difficult task for<br>
a newbie like me and probably would take quite some
time, so I’d like to<br>
know beforehand if what I want to do is reasonable.
Unfortunately, I<br>
don’t have much time until I graduate, so if it’s not
reasonable I’d<br>
have to think about other alternatives. I would really
appreciate if<br>
anyone could help me with this.<br>
</div>
</blockquote>
<br>
<div class="HOEnZb">
<div class="h5">
This sounds very complicated.<br>
<br>
It would be good if you could explain what it is that
you want to achieve with these interactions?<br>
That way you may benefit from the combined expertise of
the list members in finding a workable solution for your
problem.<br>
<br>
<br>
-- <br>
Groetjes,<br>
<br>
Anton<br>
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