[gmx-users] calculating lennard-jones interaction

[Erik Marklund]

Hi,

There is a net attractive force from vdw interactions beyond the cut-off, which can be corrected for analytically *in the case of a homogeneous system*. There is a slight artifact arising from the use of cut-offs for non-homogeneous systems such as a protein in water. Often the same corrections are used for non-homogeneous systems. It all boils down to what you want to measure, if those artifacts are large enough to ruin your investigations.


13 nov 2012 kl. 17.46 skrev Zahra M:

> thank you for your reply
> I mean the distance between two proteins is more than the cut off value,
> and in the other case the distance between two proteins is less than the cut off value,
> 
> Bests
> -Zahra
> 
> From: Erik Marklund <erikm at xray.bmc.uu.se>
> To: Zahra M <s_zahra_mousavi at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
> Sent: Tuesday, November 13, 2012 2:08 PM
> Subject: Re: [gmx-users] calculating lennard-jones interaction
> 
> Hi,
> 
> Could you rephrase the question? Distance larger than cut-off and cut-off is less than distance seem equal by definition to me.
> 
> Best,
> 
> Erik
>  
> 13 nov 2012 kl. 10.50 skrev Zahra M:
> 
>> hi dear users
>>  wanna know if the distance between two species is more than the cut off radius of vdw interaction (in a SMD simulation), can we trust the simulation results? I mean what is the difference between this case and the situation that the cut off radius is lower than the distance between two species.
>> bests.
>> Zahra
>> 
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> 
> -----------------------------------------------
> Erik Marklund, PhD
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
> phone:    +46 18 471 6688        fax: +46 18 511 755
> erikm at xray.bmc.uu.se
> http://www2.icm.uu.se/molbio/elflab/index.html
> 
> 
> 

-----------------------------------------------
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 6688        fax: +46 18 511 755
erikm at xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html