Aw: [gmx-users] C6 & C12 parameters for non-bonded interactions using tables

[Andrish Reddy]

lloyd riggs wrote
>  
> 
> Dear Andrish Reddy, 
> 
>   
> 
> Dont know if it works but I have for small molecules just put all the
> parmeters within the .top file right below the defaults, instead of user
> defined tables, and removed the "forcefieldX/SPC.itp" or
> equivalent section so it doesn't loop, but dont know if it works in
> your case.  Just a quick suggestion to try, as I parse e-mails. 
> Smone else probably has better answeres though... 
> 
>   
> 
> Stephan 
> 
> 
> Gesendet: Mittwoch, 22. Mai 2013 um 16:09 Uhr 
> Von: "Andrish Reddy" <

> areddy at .co

> > 
> An: 

> gmx-users@

>  
> Betreff: [gmx-users] C6 & C12 parameters for non-bonded
> interactions using tables 
> 
> Greetings, 
> 
> I am trying to use tabulated potentials for the VdW interactions between 
> TIP5P water molecules. 
> I have tested my topology file to make sure that it gives reasonable
> results 
> with the standard table6-12.xvg in the /top folder and C6=4*eps*sig^6 , 
> C12=4*eps*sig^12. I am able to match the energies with an identical run
> not 
> using look-up tables. The problem comes when I want to include the C6
> & C12 
> parameters within the table. This is needed for dealing with more complex 
> multi-parameter potential functions. 
> 
> I tried testing this with the standard Lennard-Jones potential. Setting 
> g(r)=-(4*eps*sig^6)/r^6 and h(r)=(4*eps*sig^12)/r^12. I then construct my 
> table according to [r,f(r),-f'(r),g(r),-g'(r),h(r),-h'(r)] 
> 
> I set vdw-type = user in my mdp file and modified my topology so that: 
> [ defaults ] 
> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 
> 1 1 yes 0.5 0.8333 
> 
> [ atomtypes ] 
> ; name at.num mass charge ptype C6 C12 
> OW_tip5p 8 16.00 0.0000 A 1.00000e+00 1.00000e+00 
> 
> Since C6 & C12 = 1, this run should be identical to using the
> table6-12.xvg 
> and C6=4*eps*sig^6 , C12=4*eps*sig^12 
> The run proceeds fine with no warnings or errors, but the LJ and Potential 
> energies are an order of magnitude higher than when using the standard 
> table. I don't understand why I am not able to reproduce the results
> by this 
> method? 
> 
> Thanks, 
> Andrish 
> 
> 
> 
> 
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Thanks Stephan, 

Don't think that will work in my case.

Andrish



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