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

[chris.neale at utoronto.ca]

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. 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.

Thank you,
Chris.

-- original message --

Mark

> On Sat, Jun 18, 2011 at 4:40 PM, chris.neale at utoronto.ca  
> <mailto:chris.neale at utoronto.ca> <chris.neale at utoronto.ca  
> <mailto:chris.neale at utoronto.ca>> wrote:
>
>     Thank you Roland.
>
>     I did use:
>
>     constraints = all-bonds
>     lincs-iter =  1
>     lincs-order =  6
>     constraint_algorithm =  lincs
>
>      From looking at the manual, I figured that angle and bond constraints
>     would all be done by LINCS if I had done (A):
>
>     pdb2gmx -vsite none
>     constraints = h-angles
>     (a combination that I have never tried)
>
>     But when I use (B):
>
>     pdb2gmx -vsite hydrogen
>     constraints = all-bonds
>
>     It seems possible to me that LINCS is not used but instead the
>     position of the atom is simply built from a mathematical function.
>     Perhaps this all stems from my lack of thorough understanding of
>     LINCS, but it seems to me that there need be no iteration to simply
>     place an atoms based on virtual_sites3 (which are constructed by
>     pdb2gms -hydrogen)
>
>     For now, I'll simply add a line to state that I built virtual sites
>     for hydrogen atoms to make it clear, but I'd still like to understand
>     the difference between options A and B, above, if you have some time.
>
>     Thank you again,
>     Chris.
>
>
>
>
>
>     On Sat, Jun 18, 2011 at 4:13 PM, chris.neale at utoronto.ca
>     <http://utoronto.ca> <
>     chris.neale at utoronto.ca <http://utoronto.ca>> wrote:
>
>     > Dear Users:
>     >
>     > If I create the topology of a peptide like this:
>     >
>     > pdb2gmx -f protein.gro -vsite hydrogens
>     >
>     > And then simulate it in vacuum, is lincs used at all? I believe that
>     > it is, as if I use a timestep that is too large then I get LINCS
>     > warnings about angles rotating more than 30 degrees, but that
>     warning
>     > message could possibly have been written with the assumption that I
>     > used LINCS and not virtual hydrogens.
>     >
>     Probably. To make sure check the constraint-algorithm selected in
>     your mdp.
>     BTW: If you want to use large timecheck you should normally use
>     constraints=all-bonds and lincs-order=6.
>
>
>     >
>     > Finally, is there a method that needs to be named or cited in
>     relation
>     > to the fact that the angles are now constrained? Is that also done
>     > with P-LINCS?
>     >
>     This is also done with P-LINCS. Not sure whether one should sign
>     something
>     regarding the construction/usage of v-sites.
>
>     Roland
>
>
>     >
>     > Thank you,
>     > Chris.
>
>