[gmx-users] Constraining two virtual sites

[Berk Hess]

Hi,

Unfortunately constraints can not be applied to virtual sites and grompp apparently
does not not check for this. I will add a check.
Constraints between virtual sites can lead to very complex constraint equations
between the masses involved. Thus the general case if difficult to implement.
Your cases seems quite simple and could be done with the pull code,
if it would support more than one reference group, which I was thinking to implement.

How many molecules do you have?

Berk

> Date: Mon, 6 Dec 2010 11:43:45 +0100
> From: fritsch at mpip-mainz.mpg.de
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Constraining two virtual sites
> 
> Hi everybody,
> 
> 
> I have some trouble setting up topology for my, I admit, quite unusual 
> system. I need to constrain the center of masses of two groups of atoms 
> to a fixed 'bond' length. Since I have to do this for every molecule I 
> cannot use the 'pull constraint' of the free energy code.
> 
> Thus in my topology I defined a com vsite for each group and tried to 
> apply a constraint between them. The atoms within each group are 
> connected by harmonic springs forming a ring polymer (for those of you 
> who know it: this is supposed to become the path integral representation 
> in the end...)
> The topol.top for a single molecule test system looks like this:
> 
> [ defaults ]
> ; nbfunc   comb-rule    gen-pairs    fudgeLJ    fudgeQQ
>   1       1        no        1.0    1.0
> [ atomtypes ]
> ;name  mass        charge    ptype  C6             C12           ; 
> sigma     epsilon
>  A      1.00800     0  A      0           0
>  B      1.00800     0  A      0           0
>  C      1.00800     0  A      0           0
>  VS     0.000       0   V      0           0
> [ moleculetype ]
> ; molname      nrexcl
> SOL        0
> [ atoms ]
> ; id at resnr resnm atnm       cgnr      charge
> 1  VS    1  A         V1        1         0
> 2  VS    1  B         V2        2         0
> 3  A     1  A         A          3         0 
> 4  B     1  A         B          4         0 
> 5  C     1  A         C          5         0 
> 6  A     1  B         A          6         0 
> 7  B     1  B         B          7         0 
> 8  C     1  B         C          8         0 
> [ virtual_sitesN ]
> ;
> 1 2 3 4 5
> 2 2 6 7 8
> [ bonds ]
> ; ai aj
> 3 4 1 0 1687
> 4 5 1 0 1687
> 5 3 1 0 1687
> 6 7 1 0 1687
> 7 8 1 0 1687
> 8 6 1 0 1687
> [ constraints ]
> ; ai   aj funct   length_A
> 1 2 1  0.1633
> [ system ]
> TEST
> [ molecules ]
> SOL     1
> 
> The conf.gro is setup such that the constraint is satisfied initially.
> 
> When I run the simulation with LINCS the constraint seem to be not 
> applied at all, the distance beetween the two vsites increases just as 
> in free diffusion. With SHAKE the system explodes immediately (without 
> error message, but every value is inf or nan).
> I am running the system with the sd integrator in (vers. 4.5.3) but also 
> tried md and no thermostat, with no change in results.
> 
> I appreciate any advice on this!
> 
> Thanks,
> Sebastian
> 
> 
> 
> 
> 
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