On 6/12/2010 9:43 PM, Sebastian Fritsch wrote:
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
I can't see anything that looks wrong. Make sure you inspect the output
of grompp thoroughly for clues about how it's interpreting the .top
file. You may like to use gmxcheck to compare the .tpr files produced
under various permutations to see that things look like they're working
correctly (remember atom numbers will start from zero in the output).
Try putting the virtual site atoms after the real atoms in the ordering.
Mark
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