[gmx-users] COM Pulling - Single Chain

Chris Neale chris.neale at utoronto.ca
Tue Oct 19 18:28:28 CEST 2010


You're right that one can not use constraints if they are also using lincs on C-C bonds.
However, constraining this bond is not necessary with a 1 fs timestep.

Even while constraining C-C bond lengths, one can still use harmonic restraints instead (also from the pull code).
Before getting any more specific replies, Joe will likely need to provide a whole bunch more information about what he
wants to do, what he has tried, what problem he has run into, etc.


-- original message --

Maybe I'm confused here, but the manual says that the pull code will not in general work for groups that have other constraints.

To quote the last part of section 6.3:

There is one important limitation: strictly speaking, constraint forces can only be calculated between
groups that are not connected by constraints to the rest of the system. If a group contains
part of a molecule of which the bondlengths are constrained, the pull constraint and LINCS or
SHAKE bond constraint algorithms should be iterated simultaneously. This is not done in GROMACS.
This means that for simulations with constraints = all-bonds in the .mdp file
pulling is, strictly speaking, limited to whole molecules or groups of molecules. In some cases this
limitation can be avoided by using the free energy code, see sec. 6.4. In practice the errors caused
by not iterating the two constraint algorithms can be negligble when the pull group consists of a
large amount of atoms and/or the the pull force is small. In such cases the constraint correction
displacement of the pull group is small compared to the bond lengths.

So it sounds like you might be OK if you use a small pull force.

The free energy code is also problematic for measuring the forces because it creates a cycle of constraints, which yields an occasional but problematic spike to huge values when trying to calculate the free energy as a function of end-to-end distance of a peptide.

Warren Gallin

On 2010-10-19, at 6:50 AM,chris.neale at utoronto.ca  <http://lists.gromacs.org/mailman/listinfo/gmx-users>  wrote:

>/  yes. use the pull code. check your convergence carefully.
/>/  --original message --
/>/  Hi All,
/>/  I was wondering if it is possible to pull on a single chain?  I would like to anchor the C-terminus and pull the N-terminus and have a plot of pulling force vs displacement.
/>/  I'm looking for more or less a yes or no answer, if you would like to elaborate then I won't complain :)
/>/  Thanks,
/>/  Joe

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