<br><font size=2 face="sans-serif">Dear David and Eirk,</font>
<br>
<br><font size=2 face="sans-serif">Thanks for the suggestions and comments.
I guess to extend the non-bonded energy exclusion list and add some kind
of volume-repulsion term might be a good idea in general, however, some
extra coding and manipulation to the rtp files seem necessary. So I will
think about other alternatives and then decide what to do. Maybe Erik will
have something ready soon.</font>
<br>
<br><font size=2 face="sans-serif">As I said, I am trying to study the
possible dewetting phenomena for a two-domain protein (within a single
chain). There are some studies by Bruce Berne, David Chandler and others
on dewetting phenomena with simple systems. For example, very recently,
Bruce's group found that for two fictious hydrophobic disks (with no charges)
inside water, there will be a dewetting layer b/w the two disks if there
is no LJ attraction, and there will still be a dewetting layer, smaller
though, if the attraction is turned on. I have found that even for the
best possible two-domain proteins (in the sense of hydrophobicity scale
analysis, i.e., strong hydrophobic groups on the domain boundaries), there
is no meaningful dewetting b/w the two-domains. Thus, I would like to see
if the deweting layer will be more noticeble if I turn off the LJ attraction
and electrostatic interactions b/w the protein and water. Without these
interactions, I expect the two domains will be further "pushed"
together and there are less incentivs for the water molecules to stay inbetween.
</font>
<br>
<br><font size=2 face="sans-serif">Ruhong</font>
<br>
<br><font size=2 face="sans-serif">Ruhong Zhou , PhD<br>
Computaional Biology Center <br>
IBM Thomas J. Watson Research Center <br>
Yorktown Heights, NY 10598 <br>
Tel: (914) 945-3591, Fax: (914) 945-4104 <br>
http://www.research.ibm.com/people/r/ruhong <br>
</font>
<br>
<br>
<br>
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<td>
<td><font size=1 face="sans-serif"><b>David <spoel@xray.bmc.uu.se></b></font>
<br><font size=1 face="sans-serif">Sent by: gmx-users-admin@gromacs.org</font>
<p><font size=1 face="sans-serif">05/21/2003 05:02 AM</font>
<br><font size=1 face="sans-serif">Please respond to gmx-users</font>
<td><font size=1 face="Arial"> </font>
<br><font size=1 face="sans-serif"> To:
gmx-users@gromacs.org</font>
<br><font size=1 face="sans-serif"> cc:
</font>
<br><font size=1 face="sans-serif"> Subject:
Re: [gmx-users] Is it possible to turn
off protein-water interaction?</font></table>
<br>
<br>
<br><font size=2><tt>On Wed, 2003-05-21 at 06:47, Erik Lindahl wrote:<br>
> Hi Ruhong,<br>
> <br>
> <br>
> No - you've probably found the concept of energy groups, but they<br>
> cannot yet be applied to individual terms.<br>
> <br>
> <br>
> However, you might soon be able to do it using groupwise decoupling<br>
> that I'm implementing for Free Energy calculations.<br>
> <br>
<br>
> I guess this is probably not supported without modifying the source,<br>
> but I will ask it anyway. Is there an easy way to turn off<br>
> protein-water interactions (vdw attraction C6 terms and Coulombic<br>
> interactions), but leave protein-protein and water-water interactions<br>
> untouched? In other words, I don't want any interactions b/w water
and<br>
> protein atoms except for the replusive LJ to avoid overlaps. I am<br>
> studying the dewetting phenomena in a multi-domain protein where two<br>
> independent domains fold into a complex structure. It would be nice
to<br>
> see what happens if there is no interaction b/w protein and water.
<br>
> <br>
You can turn off the dispersion by adjusting the parameter matrix.<br>
But... your system would explode if you leave out the compensating<br>
(attractive) terms. It would be best to switch the whole interaction off<br>
with energy_grp_excls (check exact syntax) and add another repulsion<br>
term (e.g. a hard wall, which you would have to program, and you don't<br>
want to scan through all possible interactions).<br>
<br>
Now, to understand what would happen if you make the interaction purely<br>
repulsive, my 2 c of prediction say that you would get some kind of<br>
phase separation where contact area is minimized.<br>
<br>
<br>
> <br>
> </smaller></excerpt><br>
-- <br>
Groeten, David.<br>
________________________________________________________________________<br>
Dr. David van der Spoel,
Dept. of Cell and Molecular Biology<br>
Husargatan 3, Box 596,
75124 Uppsala, Sweden<br>
phone:
46 18 471 4205
fax: 46 18 511 755<br>
spoel@xray.bmc.uu.se
spoel@gromacs.org http://xray.bmc.uu.se/~spoel<br>
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