[gmx-users] -pbc cluster with -center in trjconv 3.3.1

[chris.neale at utoronto.ca]

Hello,

I have a DPC micelle in a rhombic dodecahedron. I want to use the pull  
code relative to the center of mass of the micelle and therefore I  
need to keep all detergent monomers in the same periodic image  
(otherwise I suspect that the COM will be calculated incorrectly).

My problem is that I can not seem to get all of the detergent monomers  
into the center of a triclinic unit cell. It doesn't even need to be  
the center, just far enough from an edge that all detergents will be  
interpreted as being in the main unit cell by grompp or perhaps by  
mdrun in the very first timestep. Once I have this representation, I  
can use one pull restraint in absolute coordinates to keep the micelle  
in the unit cell and another pull restraint to do something more  
interesting.

I have been unable to get the representation that I am looking for in  
gromacs-3.3.1. I realize that gromacs-3.3.3 has an enhanced trjconv  
suite, but the -pbc cluster option in 3.3.3 and 3.3.2 sends me into an  
infinite loop and without the cluster option the -center option does  
not maintain the micelle (i.e. detergent monomers are distributed to  
the corners of the unit cell.)

I acknowledge the infinite reality of PBC, but I'll emphasize that my  
concern here is proper COM treatment. From looking at the source code  
it appears that the pull code is smart enough to look back to the  
initial frame and put things in the original box, but still I need to  
generate the correct starting frame.

To be clear about the infinite loop that I get for 3.3.2 and 3.3.3,  
here is some output:

$ ../../../../exe/gromacs-3.3.3_newccb/exec/bin/trjconv -f 100ns.gro  
-o 100ns_trjconv.gro -pbc cluster -s tpr/empty.tpr
Will write gro: Coordinate file in Gromos-87 format
Reading file tpr/empty.tpr, VERSION 3.3.1 (single precision)
Reading file tpr/empty.tpr, VERSION 3.3.1 (single precision)
Select group for clustering
Opening library file /home/cneale/gromacs/oplspope.top/aminoacids.dat
Group     0 (      System) has 29870 elements
Group     1 (         DPC) has  1150 elements
Group     2 (         SOL) has 28720 elements
Select a group: 1
Selected 1: 'DPC'
Select group for output
Opening library file /home/cneale/gromacs/oplspope.top/aminoacids.dat
Group     0 (      System) has 29870 elements
Group     1 (         DPC) has  1150 elements
Group     2 (         SOL) has 28720 elements
Select a group: 0
Selected 0: 'System'
COM:    0.144     0.000     0.000  iter = 1  Isq = 353349.094
COM:    3.672     3.528     4.600  iter = 2  Isq =  521.888
COM:    0.144     0.000     0.000  iter = 3  Isq = 353349.094
COM:    3.672     3.528     4.600  iter = 4  Isq =  521.888
COM:    0.144     0.000     0.000  iter = 5  Isq = 353349.094
COM:    3.672     3.528     4.600  iter = 6  Isq =  521.888
COM:    0.144     0.000     0.000  iter = 7  Isq = 353349.094
COM:    3.672     3.528     4.600  iter = 8  Isq =  521.888
COM:    0.144     0.000     0.000  iter = 9  Isq = 353349.094
COM:    3.672     3.528     4.600  iter = 10  Isq =  521.888
COM:    0.144     0.000     0.000  iter = 11  Isq = 353349.094
COM:    3.672     3.528     4.600  iter = 12  Isq =  521.888
COM:    0.144     0.000     0.000  iter = 13  Isq = 353349.094
COM:    3.672     3.528     4.600  iter = 14  Isq =  521.888
COM:    0.144     0.000     0.000  iter = 15  Isq = 353349.094
COM:    3.672     3.528     4.600  iter = 16  Isq =  521.888
COM:    0.144     0.000     0.000  iter = 17  Isq = 353349.094
COM:    3.672     3.528     4.600  iter = 18  Isq =  521.888
COM:    0.144     0.000     0.000  iter = 19  Isq = 353349.094
.....


Thanks if anybody has some good ideas about how I might proceed.

Chris.