[gmx-users] Electrostatics of Rigid Water

David van der Spoel spoel at xray.bmc.uu.se
Thu Aug 3 20:22:32 CEST 2006

Justin M. Shorb wrote:
> Greetings!
> I am running a modified version of Gromacs 3.3 that calls the 
> do_nonbonded subroutine twice, in order to calculate specific 
> interactions. Unfortunately for my purposes, the settle restraints 
> (which I would assume to be a 'bonded' interaction) seem to be called 
> within the nb_kernel. Is there a flag that I can reset within gromacs to 
> temporarily turn off the subroutine that runs the settle potential 
> calculation? I have been searching, but cannot seem to find where this 
> is even called. If I run a single step MD run without settle (define = 
> -DFLEXIBLE, with SPC/E force constants set to zero) then I obtain the 
> correct coulombic interaction potential, otherwise there is a discrepancy.
> Currently, the non_bonded subroutine is called using the following:
>   if (fcoul) /* added */
>       do_nonbonded(fplog,cr,fr,x,fcoul,md, /* added */
>          grps->estat.ee[egCOULSR], /* added */
>          grps->estat.ee[egCOULSR],box_size,nrnb, /* added */
>          lambda,&dvdlambda,FALSE,-1,-1,bDoForces); /* added */
> Also, I am surprised that by substituting the COULSR table where the LJ 
> table is usually passed allows for the complete neglect of LJ without 
> the (expected?) doubling of the coulombic force, although the coulombic 
> potential is doubled. I believe I read in the code that there is a check 
> in the inner loop to make sure that no forces are redundantly 
> calculated, but any further clarification would be appreciated (as this 
> was discovered empirically).

the settle algorithm is a constraint algorithm and is called from the 
update routine.

> Thanks in advance!
> Justin
> _________________________________________________________________
> Justin M. Shorb            Phone: (608) 262-0483
> Skinner Group                shorb at wisc.edu
> University of Wisconsin-Madison,  Department of Chemistry
> 1101 University Ave., Madison, WI, 53706
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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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