[gmx-users] simulations using structureless surface-2

singh singh at biophysik.chemie.uni-dortmund.de
Wed Aug 1 16:10:36 CEST 2007

Dear Erik,
The wall which I want to introduce will interact with 9-3 potential only and
will have no charges. 
Will it be more appropriate to calculate it where the nonbonded interactions
are calculated in gromacs (nonbonded.c ?)  and then update the total
potential energy?
In principle it sounds "simple" but I totally get lost as soon as I open
Is there any other place where it will be relatively easier to implement it?

With Regards,
Gurpreet Singh

University of Dortmund
Department of Chemistry
Physical Chemistry I  -  Biophysical Chemistry
Otto-Hahn Str. 6
D-44227 Dortmund
Office:   C1-06 room 176
Phone:  +49 231 755 3916
Fax:     +49 231 755 3901
-----Original Message-----
From: Erik Marklund [mailto:erikm at xray.bmc.uu.se] 
Sent: Friday, July 27, 2007 9:54 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] simulations using structureless surface-2

There was a tutorial on implementing a z-dependent electric potential  
on the gromacs web page not that long ago. It didn't seem that  
difficult. That should serve as a good starting point for your wall  
o' carbon.


27 jul 2007 kl. 01.56 skrev Mark Abraham:

>> Dear gmx users,
>> my apologies for the previous post. I will try to rephrase my  
>> problem.
>> Is it possible to introduce a plane in a particular direction, for  
>> example
>> in z direction, where molecules interact with it only based on the
>> perpendicular distance between the molecules and the plane?
> Yes, this is possible to do, but it is not implemented. Possibly  
> something
> in the distance restraints section may do what you want. See the  
> manual.
>> Is it also possible to specify the user defined potential for  
>> interaction
>> between the plane and molecules?
> Possible, but not implemented.
>> The idea is to simulate a surface, for example a graphite surface,  
>> but
>> rather than using a detailed atomistic model for it, I would like to
>> represent it by using a plane with some interaction potentials.
> If you're not dealing with only a handful of species interacting  
> with such
> a surface, you might want to write such code yourself. Otherwise,  
> you'll
> need to get your hands very dirty with GROMACS.
> Mark
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Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,	75124 Uppsala, Sweden
phone:	+46 18 471 4537		fax: +46 18 511 755
erikm at xray.bmc.uu.se	http://xray.bmc.uu.se/molbiophys

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