The prevailing wisdom, at least in AMBER, is that you should almost never
include explicit ions in implicit solvent simulations (maybe if they are
strongly associated, etc. but that is a special case). You will probably
not get physical results if you do include them.
Also, depending on the force field you are using, I think igb=8 is
generally a superior model and the new standard.
Regards,
Brian
On Mon, Oct 1, 2012 at 4:36 PM, Sajeewa Pemasinghe <sajeewasp.gmail.com>wrote:
> Hi all,
>
> I am running MD on a protein having about 3400 atoms. I am going to use
> implicit solvation (igb=7). The protein has an unperturbed charge of (-10).
> If I add 10 Na+ ions to neutralize will I have to consider that when
> specifying the value of saltcon in generalized Bone model? This might
> sound silly but the manual says that saltcon specifies the concentration(M)
> of 1-1 mobile counterions in solution. So if I add 10 Na+ ions how should I
> determine the value for saltcon?
>
> Thank you
>
> Sajeewa Dewage
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>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Mon Oct 01 2012 - 14:00:02 PDT
