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

[Mark Abraham]

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
>>