[gmx-users] is lincs used with virtual hydrogens?

[Mark Abraham]

On 20/06/2011 1:23 AM, chris.neale at utoronto.ca wrote:
> Dear Mark:
>
> Now I am confused. Your first post indicated that P-LINCS did the 
> angle constraints. But here you indicate that the v-site algorithm 
> does it.

No... my second email observed that LINCS warnings can result when 
v-sites are being used, and I ascribed that effect to the size of the 
time step. I didn't say v-sites were doing anything with angle constraints.

> This is probably because my first post was incomplete about the method 
> that I used.
>
> Can you please confirm my current understanding?
>
> Therefore (A):
>
>      pdb2gmx -vsite none
>      constraints = h-angles
>      constraint_algorithm =  lincs
>
> --> P-LINCS constrains all bonds and angles involving hydrogens
>
> But when I use (B):
>
>      pdb2gmx -vsite hydrogen
>      constraints = all-bonds
>      constraint_algorithm =  lincs
>
> --> Hydrogens are built as V-sites and P-LINCS constrains all bonds 
> that do not involve hydrogen.
>
> Of course, water is treated by SETTLE in both of the above.
>
> Please note that I am not concerned about getting LINCS warnings. I 
> probably should not have mentioned that. I am simply trying to figure 
> out exactly how to write my methods section.

Both the above are correct understandings.

I think you misread my second email. I'd intended to put my 
parenthetical observation about LINCS in the first email, but forgot to 
(however you seem to have understood my context fine). Sorry for 
whatever. :)

Mark