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.
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