[gmx-users] Pulling

mohsen ramezanpour ramezanpour.mohsen at gmail.com
Sat Mar 19 06:10:38 CET 2011

Thank you again for your reply

On Wed, Mar 16, 2011 at 7:35 PM, <chris.neale at utoronto.ca> wrote:

> 2-When you limit your sampling phase space,it can make some Errors,
>> Because you may ignore some important regions(where you don't know them
>> and you can't predict there).
> I agree with the idea that underlies your point, but it is not a problem.
> You don't need to sample all intervening phase space, just converge one well
> defined part of it. Read that paper again, and some others.
> ... snip ...
>  Is it possible to do Umbrella Sampling while the drug be free to rotate
>> along with oscilation in windows?
> sure, but you will have more convergence problems.
> Chris.
> On Tue, Mar 15, 2011 at 9:49 AM, <chris.neale at utoronto.ca> wrote:
>  1. yes. it is acceptable. It is different, but neither method is de facto
>> better.
>> 2. to enhance convergence by limiting the amount of phase space that must
>> be sampled. Changing the restraints can change the profile, but if you
>> care
>> only about the integrated standard binding free energy then it does not
>> change the converged result. See, for example, D. L. Mobley, J. D.
>> Chodera,
>> K. A. Dill. "On the use of orientational restraints and symmetry number
>> corrections in alchemical free energy calculations", ...
>> Chris.
>> -- original message --
>> Dear All
>> Afew question about Pulling in Umberella Sampling
>> 1-the goal of pulling is making some primary structures (in different
>> distances) to do umberella sampling for each one of them.
>>  I can make these states by transporting my ligands along a vector to
>> prepare these primary structures.Is this correct?Now I can do US for each
>> one!without any need to doing pulling.
>> 2-Why do we keep fix the relative orientation of Protein-ligand during the
>> pulling ? I think changing the orientation of ligand during the
>> pulling(suppose the protein is restrain) can chang our result?
>>  Because our umbrella sampling maintain this orientation too.am I right?
>> Thanks in advance
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