[gmx-users] Is it possible to turn off protein-water interaction?

Ruhong Zhou ruhongz at us.ibm.com
Wed May 21 17:36:01 CEST 2003

Dear David and Eirk,

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.

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. 


Ruhong Zhou , PhD
Computaional Biology Center 
IBM Thomas J. Watson Research Center 
Yorktown Heights,  NY 10598 
Tel: (914) 945-3591, Fax: (914) 945-4104 

David <spoel at xray.bmc.uu.se>
Sent by: gmx-users-admin at gromacs.org
05/21/2003 05:02 AM
Please respond to gmx-users
        To:     gmx-users at gromacs.org
        Subject:        Re: [gmx-users] Is it possible to turn off 
protein-water   interaction?

On Wed, 2003-05-21 at 06:47, Erik Lindahl wrote:
> Hi Ruhong,
> No - you've probably found the concept of energy groups, but they
> cannot yet be applied to individual terms.
> However, you might soon be able to do it using groupwise decoupling
> that I'm implementing for Free Energy calculations.

> I guess this is probably not supported without modifying the source,
> but I will ask it anyway. Is there an easy way to turn off
> protein-water interactions (vdw attraction C6 terms and Coulombic
> interactions), but leave protein-protein and water-water interactions
> untouched? In other words, I don't want any interactions b/w water and
> protein atoms except for the replusive LJ to avoid overlaps. I am
> studying the dewetting phenomena in a multi-domain protein where two
> independent domains fold into a complex structure. It would be nice to
> see what happens if there is no interaction b/w protein and water. 
You can turn off the dispersion by adjusting the parameter matrix.
But... your system would explode if you leave out the compensating
(attractive) terms. It would be best to switch the whole interaction off
with energy_grp_excls (check exact syntax) and add another repulsion
term (e.g. a hard wall, which you would have to program, and you don't
want to scan through all possible interactions).

Now, to understand what would happen if you make the interaction purely
repulsive, my 2 c of prediction say that you would get some kind of
phase separation where contact area is minimized.

> </smaller></excerpt>
Groeten, David.
Dr. David van der Spoel,                 Dept. of Cell and Molecular 
Husargatan 3, Box 596,                   75124 Uppsala, Sweden
phone:           46 18 471 4205                          fax: 46 18 511 
spoel at xray.bmc.uu.se             spoel at gromacs.org   
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