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Simulations with constant dielectric
#37790 12/22/19 08:07 PM
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pmj Offline OP
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Hi!

In case I want to preform simulations in vacuum, I should just remove solvent I am using, but what would be a standard command in case I would like to apply a constant dielectric of for example 40.0, to better describe the electrostatics?

Should I just use NONBONDED cdie 40.0 or there are extra keywords I should use with it?

Thanks

Re: Simulations with constant dielectric
pmj #37791 12/23/19 10:48 AM
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Well, if you truly want to simulate your system in vacuum then you should use CDIE EPS 1.0.

If you just want to avoid the cost of using explicit solvent you could try one of the implicit solvent models. Just changing epsilon is not the right thing to do (which is why it is never done). EPS 40.0 would strongly affect all short-range electrostatic interactions in a very non-physical way, you would for instance most likely loose all hydrogen bonds...


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: Simulations with constant dielectric
lennart #37792 12/23/19 12:19 PM
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pmj Offline OP
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Dear Lennart,

I am already using GBSW implicit solvent, but it is not as fast as we expected, because the system is rather large.

We wanted to simulate the same system with constant dielectrics of around 40.0 or 80.0, which I know it is not as accurate as implicit or explicit solvent, but should be more accurate than vacuum simulation.

I am just wondering what command line should I use (for example in GBSW there is a recommended non bonded keywords that one should use). I assume just CDIE EPS 40.0 won't do?

Thanks

Re: Simulations with constant dielectric
pmj #37793 12/25/19 02:12 PM
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There are other implicit solvent methods that may be faster.

Explicit solvent simulations on a GPU (< 1000$) are very fast and in many cases faster than implicit solvent simulations.

I think it would be very difficult to publish a paper using CDIE EPS 40.0 (or any vacuum simulation).


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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