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

Qikai Li qkli at iccas.ac.cn
Mon May 21 05:18:31 CEST 2007

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).

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];


Best regards,


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