It might, but i would still want precision estimates for the 2 setups
before you explore other differences. Until you can get a reproducible
profile, comparisons will be uncertain.
On Fri, Nov 22, 2024, 8:51 PM Ramdhan,Peter A <pramdhan1.ufl.edu> wrote:
> Would the starting reaction coordinate matter? Is there a way to correct
> for the difference in starting distances or does the QM/ASMD "account" for
> that?
>
>
> Sincerely,
>
> *Peter Ramdhan*
> ------------------------------
> *From:* Carlos Simmerling <carlos.simmerling.gmail.com>
> *Sent:* Friday, November 22, 2024 8:45 PM
> *To:* Ramdhan,Peter A <pramdhan1.ufl.edu>
> *Cc:* AMBER Mailing List <amber.ambermd.org>
> *Subject:* Re: [AMBER] question about steered MD
>
> *[External Email]*
> I see, then I would start by doing independent runs to get uncertainties.
>
> On Fri, Nov 22, 2024, 7:28 PM Ramdhan,Peter A <pramdhan1.ufl.edu> wrote:
>
> Hi Carlos,
>
> Sorry for not being more specific. I am using a combined QM/SMD with
> ORCA/AMBER. My input uses the &smd namelist. From the output file, I get
> "work" in the 5th column. Then, I have been using the scripts from the
> ASMD tutorial for generating the jar average (
> https://ambermd.org/tutorials/advanced/tutorial26/index.php) but of
> course modifying the script to get the pertinent output from the &smd
> output. I believe I have been doing this part correctly.
>
> Snippet from smd output:
>
> #
> # MD time (ps), CV, handle_position, spring_constant, work
> #
> 0.0000 8.59307148 8.58000000 1000.00000000
> 0.00000000
> 0.0010 8.59219145 8.57997936 1000.00000000
> 0.00026095
> 0.0020 8.59117660 8.57991762 1000.00000000
> 0.00098546
>
>
> From the averages calculated, I use the stitch PMF py script, to get the
> full PMF.
>
> Sincerely,
>
> *Peter Ramdhan*
> ------------------------------
> *From:* Carlos Simmerling <carlos.simmerling.gmail.com>
> *Sent:* Friday, November 22, 2024 7:23 PM
> *To:* Ramdhan,Peter A <pramdhan1.ufl.edu>; AMBER Mailing List <
> amber.ambermd.org>
> *Subject:* Re: [AMBER] question about steered MD
>
> *[External Email]*
> Steered md itself doesn't give a pmf, how are you doing that?
> Also make sure you have error bars on both pmfs, to make sure those are
> smaller than the differences from mutation.
>
>
> On Fri, Nov 22, 2024, 7:09 PM Ramdhan,Peter A via AMBER <amber.ambermd.org>
> wrote:
>
> Hello,
>
> I am using a steered MD to steer a substrate to the reaction center of a
> heme-containing enzyme. I am using a LCOD as the rxn coordinate. I am
> comparing the wild-type PMF to that of two mutants. Is there a way to
> compare across different starting rxn coordinates. For example, the LCOD
> for the substrate to the heme is 8 angstroms total while the LCOD for the
> same substrate in the mutant is 6 angstroms total. Is there a way to
> correct for the differences in initial distances? I found that the PMF is
> much larger in the wild-type than the mutant and I think it might be
> because of the wild-type having to travel a larger distance based on my
> initial ASMD start.
>
> Sincerely,
>
> Peter Ramdhan
>
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>
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Received on Sun Nov 24 2024 - 08:30:02 PST
