[gmx-developers] on extracting atomic force data for PMF analysis

[David van der Spoel]

Qikai Li wrote:
> Recently, I've had a look at the source codes, I'd like to extract the  
> component force data, for example, water - water electrostatic 
> interactions, water - water LJ interactions, water - nanotube 
> electrostatic interactions, and water - nanotube LJ interactions et al, 
> for PMF (potential of Mean force) analysis, which is quite similar to 
> the calculations of energy groups. All the nonbond interactions are 
> handled by a bunch of  MASM codes (except the PPC version). To modify 
> the assembly codes, I'm afraid that I might  make some mistakes on the 
> nonbond calculation kernels. I wonder if you have any C codes  for  the 
> corresponding nonbond calculations. Or you may give me some hints on how 
> to handle such kinds of problems.
> 
> In reading the codes, I have a general feeling that there are far too 
> many calling parameters, and the structures may be streamlined (I hope).
>

why not use the standard PMF methods that are implemented?


> Also, in reading the codes, I've found the following may be a bug:
> in ns.c
> +++++++++++++++++++++++++++++++++++++++++++++++
>        if (bfree)
>        {
>            nl->il_code = eNR_NBKERNEL_FREE_ENERGY;
>        } else
>        {
> 
>            /* Ewald uses the standard tabulated loops */
>            if (icoul==5)
>            {
>                icoul==3;                           ==========>    icoul 
> = 3;                      }
> 
>            nn = inloop[4*icoul + ivdw];
> 
> +++++++++++++++++++++++++++++++++++++++++++++++
Hm, this could well be wrong indeed.

> 
> Best regards,
> 
> Qikai
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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