Sindrila,
Please don't double post to the list.
(i) It's certainly possible that the starting structure is
thermodynamically unfavorable given the sampling potential (*i.e.* with
restraints). Whether or not this is "correct" is pretty much up to the
user.
MM force fields are usually robust enough to quickly relax to a more
plausible configuration while QM/MM potentials are often inclined to fail
gloriously and predict chemistry never before known to man. Personally, I
would recommend, at the very least, inspecting several (or all) of the
trajectories at the outset to verify that they look "correct" to you.
(ii) All AMBER nmropt restraints are read from &rst namelists in the file
specified by DISANG. To add multiple restraints simply add additional
namelists. This should be well documented in the manual.
(iii) I am not sure what you mean here. I think the answer to (i) above
covers this as the starting structure is the starting structure, regardless
of how it is generated. One might be able to make subjective arguments
about how "correct" a starting structure is, but this is essentially left
to the user.
That being said, you may certainly get completely different results
depending on the equilibration protocol that goes into generating the
starting structure. If you are performing a 1d umbrella sampling, I have
occasionally found it useful to use the "jar" option to slowly change the
potential in a non-equilibrium fashion. Presumably if the driving rate is
not too fast (that is meant to be as ambiguous as it sounds) then the
equilibrium of the starting structure is minimally perturbed and it should
be "correct".
Regards,
Brian
On Fri, Feb 8, 2013 at 12:30 PM, Sindrila Dutta banik <
sindrila.duttabanik.yahoo.com> wrote:
> Dear all,
> In the manual for the umbrella sampling an example is given for a
> torsional angle restrain.
> As I understood from the manual
> and tutorial that first I have to generate different windows (having
> different angle value), then for each window minimize, equilibrate,
> production run with saving DUMPAVE. Then from this files generate the PMF.
>
> Now I want to know
> (i) If I apply a restrain by DISANG command it will create a strained
> structure. Is it correct?
> (ii) How to apply two restrain simultaneously? what should be TYPE for
> this? DISTANCE? (iii) Is it possible to apply restrain gradually?
> (iv) If I apply restrain gradually then also I have to perform
> equilibrate, production run?
>
> With best regards
> Sindrila
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
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Department of Chemistry : Piscataway, NJ
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radak004.umn.edu :
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Received on Fri Feb 08 2013 - 10:30:03 PST
