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

[Mark Abraham]

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
>>>>