Virtual_sites3 "Automatic Parameters"?

User discussions
1

According to the documentation for virtual site parameters here: Particle type — GROMACS 2019-rc1 documentation

It indicates there should be parameters specified
“with the parameters specified (last one, two or three columns a b . . )”.

However in this documentation pdb2gmx input files — GROMACS 2021 documentation

It says “Note that we do not have to specify the actual parameters (that is automatic), just the type of mass center to use.”

I really want these “automatic” or default parameters to be included in the itp files that come out of pdb2gmx ... -vsite hydrogens but these parameters are blank under c0 c1 c2. Examples below. How do I make these itp files include these automatic parameters? Also how can a function be -3 or -4??

[ virtual_sites3 ]
;  ai    aj    ak    al funct            c0            c1
    3     7     1     2     1 
    4     7     1     2     1 

[ virtual_sites3 ]
;  ai    aj    ak    al funct            c0            c1
   20    19    17    21     2 
   33    32    29    34     2 

[ virtual_sites3 ]
;  ai    aj    ak    al funct            c0            c1
   15    14    12     9     3 
   16    14    12     9    -3 

[ virtual_sites3 ]
;  ai    aj    ak    al funct            c0            c1            c2
    5     7     1     2    -4 
    6     7     1     2     4 
   10     9     7    12     4 
   11     9     7    12    -4 

[ virtual_sites4 ]
;  ai    aj    ak    al    am funct            c0            c1            c2
    8     7     3     9    17     2 
   22    21    19    23    41     2 
   46    45    43    49    53     2
2

Hi,
One way to see the values generated for vsite is to extract them using gmx dump of a tpr file, generated from that topology
Kind regards
Alessandra

3

Thanks,

At least I can get them :). I wish there was an easy way to get these into the itp files. Seems silly to have to parse a complicated dump file to add them. Since for instance the itp files are 1-indexed while this dump is 0-indexed. Also kind of annoying that all the virtual_sites3 in the itp file are simply labelled [ virtual_sites3 ] (for 3, 3fd, 3fad, & 3out) with the function number below instead of like in the dump they are under for instance Virtual site 3fd and VSITE3FD. Probably would have done better in the topology code to have it labelled [ virtual_sites3 ], [ virtual_sites3fd ], [ virtual_sites3fad ], [ virtual_sites3out ].

Also my parameters in the dump for virtual_sites3fad look wrong. For function 3 according to the docs there should be an angle value theta and a vector length |d| but all I see is a value for a parameter a and b and they are all the same with a=-5.00000007e-02 and b= 8.66025388e-02 as showing below. This seems like a bug so I will report to gitlab.

image
image1356×199 45 KB

Background is I am testing gmx_MMPBSA with virtual sites which makes use of all the angles and bond lengths.

4

Posted follow up on gitlab Question on gmx dump for VSITE3FAD parameters (#4625) · Issues · GROMACS / GROMACS · GitLab