[gmx-users] Virtual Sites

[Roland Schulz]

Hi,

I haven't tried it but it should work if you set verlet-buffer-drift=-1 and
set rlist manually.

Roland


On Mon, Dec 2, 2013 at 3:20 PM, Brad Van Oosten <bv07ay at brocku.ca> wrote:

> I am trying to add virtual sites to a simulation with no mass or charge,
> just
> to make tracking the center of mass of groups later easier later on.
>
> However, I keep getting the warning "The mass of a vsiten constructing atom
> is <= 0" when i run grompp.
>
> Here's the section of my .itp file where i have defined them:
>
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB
> chargeB      massB
> ; residue   1 CHX rtp CHX  q  0.0
>      1       CLAL      1    CHX    CL1      1     -0.151     35.453   ;
> qtot
> -0.151
> .
> .
> .
> .
>
>     63         CA      1    CHX    CZ2     63      0.083     12.011   ;
> qtot
> 0.144
>     64       CLAL      1    CHX    CL2     64     -0.144     35.453   ;
> qtot
> 0
>     65       MCH3      1    CHX     V1     65          0          0   ;
>     66       MCH3      1    CHX     V2     66          0          0   ;
>     67       MCH3      1    CHX     V3     67          0          0   ;
>     68       MCH3      1    CHX     V4     68          0          0   ;
>     69       MCH3      1    CHX     V5     69          0          0   ;
>     70       MCH3      1    CHX     V6     70          0          0   ;
>     71       MCH3      1    CHX     V7     71          0          0   ;
>     72       MCH3      1    CHX     V8     72          0          0   ;
>     73       MCH3      1    CHX     V9     73          0          0   ;
>     74       MCH3      1    CHX    V10     74          0          0   ;
>     75       MCH3      1    CHX    V11     75          0          0   ;
>     76       MCH3      1    CHX    V12     76          0          0   ;
>
> [virtual_sitesn]
>     65  2       8 9 10 11
>     66  2       2 3 6 7
>     67  2       1 4 5 12 13
>     68  2       14 15 16 17 18
>     69  2       19 20 21 22 23
>     70  2       24 25 26 27 28 29 30 31 32
>     71  2       33 34 35 36 37 38 39 40 41
>     72  2       49 50 51 52 53
>     73  2       44 45 46 47 48
>     74  2       42 43 54 57 58
>     75  2       55 56 59 60
>     76  2       61 62 63 64
>
>
> Am I defining something wrong here?
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/Virtual-Sites-tp5012975.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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