VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Mar 29 2018 - 12:58:02 CDT

On Thu, Mar 29, 2018 at 12:40 PM, Brian Radak <brian.radak_at_gmail.com> wrote:
> I don't think there are any tools for this integrated with VMD at present
> (or at least not as part of the normal distribution). Maybe try packmol?

there is a tutorial for how to build and equilibrate simple molecular
liquid boxes with VMD and TopoTools here:
https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---part-2
this uses OPLS/AA, but that doesn't make much of a difference as those
systems will have to be re-quilibrated after solvation anyway.

the effect of a specific pH is usually not possible to model in the
solvent (and not worth trying), but through choices as to how residues
are protonated due to the pKa / pKb of the side chains.

axel.

> I have seen simulations with tetrachloroethane, but only as part of the
> highly mobile membrane-mimetic (HMMM) model. Maybe someone from the
> Tajkhorshid group can point to how those are built?

>
> HTH,
> BKR
>
>
> On Thu, Mar 29, 2018 at 11:50 AM, Alex Saad-Falcon
> <alexsaadfalcon_at_gmail.com> wrote:
>>
>> Hello all,
>>
>> How can I find PDB and PSF files for non-water solvents? Ideally, I want a
>> range of pH values from ~6.5-8.5, but any help on where to find a solvent
>> other than water would be greatly appreciated.
>>
>> Thanks,
>>
>> Alex
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.