[gmx-users] anomalous free energy dgdl.xvg values every nstlist steps while using a twin-range cutoff

[Berk Hess]

Hi,

This was a new issue in 4.0, 3.3 was fine.

Berk

> Date: Wed, 18 Feb 2009 13:26:39 -0500
> From: chris.neale at utoronto.ca
> To: gmx-users at gromacs.org
> Subject: [gmx-users] anomalous free energy dgdl.xvg values every nstlist	steps while using a twin-range cutoff
> 
> Thanks Berk, 4.0.4 does show the expected behaviour for me with the  
> twin-range cutoff. Since I obtained 4.0.4 prior to mentioning this  
> issue, I gather that you gave the free energy code a good looking-over  
> recently. I really appreciate it.
> 
> I have seen only one previous paper that utilized a twin-range cutoff  
> for annihilation simulations, but that was done via gromos in 2003  
> (Lei and Smith, Biophys. J., 3513-3520, 2003) and since this part of  
> the free-energy code in gromacs is done in C, not fortran, I expect  
> that gromos annihilation simulations utilizing a twin-range cutoff are  
> not necessarily subject to any of these issues.
> 
> Thanks again,
> Chris.
> 
> -- original message --
> 
> Hi,
> 
> I just fixed this in 4.0.4.
> The forces are always correct, dgdl in 4.0.3 was only correct at  
> nstlist steps.
> 
> Currently 4.0.4 is only available through ftp.
> We still need to add it (and the release notes) to the download page.
> 
> Berk
> 
> > Date: Tue, 17 Feb 2009 17:50:17 -0500
> > From: chris.neale at utoronto.ca
> > To: gmx-users at gromacs.org
> > Subject: [gmx-users] anomalous free energy dgdl.xvg values every  
> > nstlist steps while using a twin-range cutoff Hello,
> >
> > I believe that the free-energy code dgdl contribution from the  
> > twin-range cutoff is being calculated incorrectly in gromacs 4.0.3  
> > (and probably other versions as well).
> >
> > Specifically, I notice that the dgdl values spike at nstlist  
> > intervals. This can be seen directly from my dgdl.xvg and also from  
> > running g_analyze -ac.
> >
> > I suspect that while the forces from the LJ interactions that are in  
> > the longer range of the twin-range are added every step while the  
> > dgdl value is modified to have nstlist times these contributions  
> > every nstlist step.
> >
> > My belief that the forces are truley added every step comes from  
> > section 4.6.3 of the gromacs 4 manual:
> >
> > "In the neighbor list all interaction pairs that fall within rlist  
> > are stored. Furthermore, the interactions between
> > pairs that do not fall within rlist but do fall within  
> > max(rcoulomb,rvdw) are computed during NS, and the forces
> > and energy are stored separately, and added to short-range forces at  
> > every time step between successive NS."
> >
> > Perhaps the long-range LJ component forces are actually applied to  
> > the particles every nstlist steps as a force multipled by nstlist,  
> > as is done in NAMD, but I am currently under the impression that  
> > this is not the case.
> >
> > I am happy to provide more details and files if necessary, but  
> > hopefully this information is sufficient for a skilled coder to take  
> > a look and determine if this is indeed the case.
> >
> > Thank you,
> > Chris.
>   -- snip --
> 
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