[gmx-users] Re: energy conservation: shift vs shifted user potential

[Anja Kuhnhold]

Ok, that didn't help me much.
Of course I changed both, potential and force to shifted ones.
And sure I used a little fortran code to generate the tables --

I have found the problem:
I thought GROMACS would ignore the table values above the cutoff distance,
but it does not.
I added zeros and now it works.

Thanks anyway
Anja




> ----- Original Message -----
> ----- Original Message -----
> From Mark Abraham <Mark.Abraham at anu.edu.au>
> Date Sat, 09 Jun 2012 12:59:17 +1000
> To Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject Re: [gmx-users] Re: Re: energy conservation: shift vs 
> shifted	user potential
> On 9/06/2012 2:05 AM, Anja Kuhnhold wrote:
> > Ok, I try to explain it again :)
> > I know the format of the user tables (x, f(x), -f'(x), g(x), -g'(x), 
> h(x), -h'(x);
> > f is coulomb, g dispersion, h repulsion).
> > For testing the simple cut-off version, my table looks like the
> > example in the installation.
> > So I run a simulation with vdwtype=cut-off
> > and the same with vdwtype=user.
> > The results are the same.
> >
> > The problem is, that I want to use shifted forces and potentials 
> within my tables.
> > (Aim is better energy conservation)
> > In the manual (ch. 4.1.5) is explained how the shift functions
> > for forces and potentials have to be.
> > So for -g(x) and h(x) I use the potential from the manual, Phi, with 
> alpha=6 and 12, respectivly.
> > And for g'(x) and -h'(x) I use the shifted force from the manual, 
> Fs, with alpha=6 and 12, respectivly.
> > But when I run the simulation with this table on the one hand
> > and with vdwtype=Shift on the other hand,
> > the results are not comparable, mostly the energy is not conserved 
> by using the table.
> 
> The force is the negative derivative of the potential. If you change 
> only the force columns then you have made the interaction piecewise 
> discontinuous at every segment. So when GROMACS uses both the values 
> and 
> derivatives to convert your table into the internal format used 
> (section 
> 6.7.1), it comes up with junk. There should be a warning printed if 
> the 
> force column is not close enough to the numerical derivative of the 
> potential column, but maybe this change is close enough that you avoid 
> 
> that. Anyway, this makes energy basically impossible to conserve. You 
> 
> should generate all your table values from the actual function you 
> wish 
> to implement, e.g. with a spreadsheet or scripting language.
> 
> Mark
> 
> >
> > Can you follow me?
> >
> > Anja
> >
> >
> >
> > ----- Ursprüngliche Nachricht -----
> > Von: gmx-users-request at gromacs.org
> > Datum: Freitag, Juni 8, 2012 15:55
> > Betreff: gmx-users Digest, Vol 98, Issue 52
> > An: gmx-users at gromacs.org
> >
> >> ----- Ursprüngliche Nachricht -----
> >> Von Mark Abraham<Mark.Abraham at anu.edu.au>
> >> Datum Fri, 08 Jun 2012 23:40:35 +1000
> >> An Discussion list for GROMACS users<gmx-users at gromacs.org>
> >> Betreff Re: [gmx-users] Re: energy conservation: shift vs shifted user
> >> potential
> >> On 8/06/2012 5:59 PM, Anja Kuhnhold wrote:
> >>> Hello all,
> >>>
> >>> can someone give me a hint, please?
> >>> Do you need more information?
> >>> Has anyone had a similar problem.
> >>>
> >>> I really need to figure that out, because I will simulate other systems
> >>> which can be run only with user tables.
> >>>
> >>> Anja
> >>>
> >>>
> >>>
> >>> -
> >>>> ----- Original Message -----
> >>>> ----- Original Message -----
> >>>>  From Anja Kuhnhold<anja.kuhnhold at physik.uni-halle.de>
> >>>> Date Wed, 06 Jun 2012 15:07:40 +0200
> >>>> To gmx-users at gromacs.org
> >>>> Subject [gmx-users] energy conservation: shift vs shifted user potential
> >>>> Dear gmx-users,
> >>>>
> >>>> I have a problem concerning energy conservation when using user
> >>>> potentials (tables).
> >>>> I'm using gromacs 4.5.4
> >>>> I simulate a simple Lennard-Jones(6-12) +Fene polymer melt (1600
> >>>> chains a 10 beads in a 26x26x26 periodic box).
> >>>>
> >>>> I tried different vdwtypes (cutoff always 3.24):
> >>>> The cut-off version does not conserve energy -- okay.
> >>>> The shift and switch versions conserve energy -- fine.
> >>>>
> >>>> Now I wanted to do the same with user tables:
> >>>> Simple Lennard-Jones table gives really the same results as the
> >>>> cut-off version -- good.
> >>>>
> >>>> But if I use a table with shifted Lennard-Jones potential it is not
> >>>> comparable to the shift version
> >>>> and the energy is not conserved -- ?
> >>>>
> >>>> I use a shift function as written in the manual (chapter 4.1.5) --
> >>>> there must be a factor alpha added in the constants A and B --
> >>>> (r1=0).
> >>>>
> >>>> The parameters are the same for shift version and shifted user version.
> >>>>
> >>>> Has someone an idea why the shifted user potential doesn't work in
> >>>> this way?
> >> We've no real idea what you've done... manual 6.7.2 describes the
> >> required format and there are (unshifted) examples in your
> >> installation
> >> under $GMXLIB/share/top/table*.xvg.
> >>
> >> Makr
> >>
> >>>> Here is the mdp:
> >>>>
> >>>>
> >>>> integrator        	= md-vv
> >>>> dt                	= 0.0035
> >>>> nsteps                	= 1000
> >>>> nstxout                	= 1
> >>>> nstvout                	= 1
> >>>> nstfout                	= 1
> >>>> nstlog                	= 1
> >>>> ns_type                	= grid
> >>>> pbc                	= xyz
> >>>> rvdw                	= 3.24
> >>>> rlist                	= 3.6
> >>>> tcoupl                	= no
> >>>> tc-grps                	= System
> >>>> tau_t                	= 2.0
> >>>> ref_t                	= 127.2717
> >>>> vdwtype                	= user;Shift
> >>>> rcoulomb        	= 3.6;2.24;1.12
> >>>> coulombtype        	= Cut-off
> >>>> rvdw-switch        	= 0.0
> >>>>
> >>>> energygrps        	= bead
> >>>> energygrp_table        	= bead bead
> >>>>
> >>>>
> >>>> Thanks in advance
> >>>> Anja
> >>>>