Ah okay thank you!
I have an additional question regarding the preparation of large systems
using Packmol Memgen. Actually trying to work with a really big
multi-subunit complex I could insert it into the membrane but on the next
step I had a problem with tleap parametrization (activated directly in the
packmol memgen), which was related to lipids (.. big distances between some
of them). I also checked my structure (without the membrane) using tleap
and apparently there was no problem with it.
Thank you in advance!
Enrico
Il giorno gio 16 mag 2024 alle ore 13:38 Carlos Simmerling <
carlos.simmerling.stonybrook.edu> ha scritto:
> Since implicit solvent simulations don't employ PME, a cutoff is not
> usually used, leading to slow simulations of large systems. per-step times
> are usually faster with explicit water, and the advantage comes from faster
> sampling rates in implicit solvent. So I don't think this would be helpful
> for you, at least not without additional optimizations of the implicit
> solvent code to speed up long-range interactions (for example, Alexey
> Onufriev has done work in that area).
>
>
> On Thu, May 16, 2024 at 5:02 AM Enrico Martinez via AMBER <
> amber.ambermd.org> wrote:
>
>> Dear Amber users !
>>
>> I am working on a membrane protein tutorial using packmol-memgen for
>> creation of a quite big system. Due to the size of the system I wonder if
>> it would be possible to ignore the adding water in the system to perform
>> simulation using implicit solvent. What options should be provided for
>> packmol ?
>>
>> Many thanks in advance
>>
>> Enrico
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>>
>
>
> --
>
> ===================================================================
> Carlos Simmerling, Ph.D.
> Professor, Department of Chemistry
> Associate Director, Laufer Center for Physical and Quantitative Biology
> Laufer Center, Room 119 Phone: 1-631-632-5424 Fax 1-631-632-5405
> Stony Brook University E-mail:
> carlos.simmerling.stonybrook.edu <carlos.simmerling.gmail.com>
> Stony Brook, NY 11794-5115 Web: http://www.simmerlinglab.org
> ===================================================================
>
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Received on Thu May 16 2024 - 08:30:02 PDT
