From: M. A (matabay2010_at_gmail.com)
Date: Sun May 31 2020 - 15:03:04 CDT
Dear Giacomo
Hi
Thank you for your guidance. It was useful.
best regards
On Sun, May 31, 2020 at 8:33 PM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:
> Hi Maryam,
>
> On Sun, May 31, 2020 at 7:33 AM M. A <matabay2010_at_gmail.com> wrote:
>
>> Dear all,
>> I am trying to run QMMM simulation without use of QWiKMD and I am doing
>> it just with config files like the MD simulation.
>>
>
> That's actually how most simulations are run. QwikMD "flattens the
> learning curve" for scientists new to MD simulation, but eventually you are
> supposed to read the user's guide, starting from the parts that you are
> interested in. The right place to begin is reading up on the subject
> introduced by the "Info" buttons of QwikMD, which I hope is what you are
> doing.
>
>
>> I have a question about version of NAMD for running QMMM simulation. can
>> we use NAMD_2.12_Linux-x86_64-multicore for this aim? or we should use the
>> newer version of NAMD? I mention it again that I dont use QWiKMD plugin.
>>
>
> Both versions 2.13 and 2.14b1 contain several improvements to QM/MM
> interface:
> https://www.ks.uiuc.edu/Research/namd/2.13/announce.html
> https://www.ks.uiuc.edu/Research/namd/2.14b1/announce.html
> and in general it is always better to use a newer version, because there
> are usually improvements across the board that affect all use cases.
>
> Giacomo
>
>
>
>> best regards
>>
>> --
>> Maryam Atabay
>> Ph.D in Nano Computational Chemistry
>> Department of Physics, Sharif University of Technology
>>
>>
>
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Research collaborator, National Institutes of Health, Bethesda, MD
> http://goo.gl/Q3TBQU
> https://github.com/giacomofiorin
>
-- Maryam Atabay Ph.D in Nano Computational Chemistry Department of Physics, Sharif University of Technology
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