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grompp renumbers atom types with the same LJ parameters.<br>
Then you should use grompp -norenum<br>
<br>
Berk<br>
<br>
On 12/13/2010 01:01 PM, Leo wrote:
<blockquote
cite="mid:AANLkTimoW-XeXmhjZJsPJ5dZ7M91Pkqf+Vcm+MWXrQDC@mail.gmail.com"
type="cite">
<div>Hi Berk,</div>
<div><br>
</div>
<div>Thanks for the quick reaply.</div>
At the moment I have a test system with 5 atoms, defined with different
atomtypes in the topology (and in the forcefield).
<div>Their values for the typeA variable change as I modify the LJ
parameters (the ones with the same parameters have the same typeA
value). So typeA is not a direct reference to the atomtypes as defined
in the topology, which is what I'm looking for.</div>
<div><br>
</div>
<div>Leo.</div>
<div><br>
<div class="gmail_quote">2010/12/13 Berk Hess <span dir="ltr"><<a
moz-do-not-send="true" href="mailto:hess@cbr.su.se">hess@cbr.su.se</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;">Hi,<br>
<br>
t_mdatoms contains an array typeA which contains the atom types.<br>
<br>
But any type of (pairwise) non-bonded interaction that depends linearly<br>
on the charges<br>
and/or LJ parameters can be passed through the user tables. This can be
made<br>
atomtype specific using the energgrp and energygrp_table mdp options.<br>
So I think you wouldn't need to do any coding at all.<br>
<br>
Berk<br>
<div>
<div class="h5"><br>
On 12/13/2010 12:28 PM, Leo wrote:<br>
> Hello,<br>
><br>
> I am trying to implement a new non-bonded interaction in GROMACS
that<br>
> should only be applied to certain atom types.<br>
> I already figured out how to modify the existing interactions and
how<br>
> to implement new forces, but I still don't know how to apply them
only<br>
> to a specific atom type. The t_mdatoms struct doesn't seem to
include<br>
> any atomnames or atomtypes variables, so I was wondering if I
should<br>
> include one (just copying it from t_atoms, in the same way as all
the<br>
> other variables are copied in the atoms2md() function) and use it
to<br>
> restrict the application of the new forces based on the
atomtypes/names.<br>
> It looks a bit complicated to handle the problem this way, so could<br>
> you think of a better solution (e.g. using the parameters already<br>
> available in the t_mdatoms struct)?<br>
><br>
> Leonardo Garma<br>
> Graduate Student<br>
> University of Oulu<br>
> Biochemistry Department<br>
><br>
><br>
><br>
><br>
<br>
</div>
</div>
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