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Originally Posted By: lennart
If you need the huge version for implicit solvent (GB) calculations, it may well be that explicit solvent is more efficient....

I'm not doing dynamics though. Monte Carlo is appropriate for the kind of sampling that I am looking for and I don't think I can perform Monte Carlo in explicit water.

Last edited by gianluca; 04/27/11 09:59 PM.
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Originally Posted By: lennart
CUTNB obviously is irrelevant for MC (well, depending on the move set it might still be useful I guess).

By "irrelevant" do you mean that it could also be set equal to or even smaller than CTOFNB?

Thanks!

Last edited by gianluca; 04/28/11 01:24 AM.
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No, that will not work.


Lennart Nilsson
Karolinska Institutet
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I think CHARMM crashes if you have CUTNB < CTOFNB

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I decided to test it. In my case, it does not crash but it produces nonsense smile

Last edited by gianluca; 04/28/11 05:20 AM.
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Originally Posted By: gianluca
I don't think I can perform Monte Carlo in explicit water.
Why not?

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Originally Posted By: Kenno
Originally Posted By: gianluca
I don't think I can perform Monte Carlo in explicit water.
Why not?

Don't you have to re-equilibrate the water molecules around the protein after each move? Or am I wrong? I would be happy for any advice. Thanks.

Last edited by gianluca; 05/06/11 11:09 PM.
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UPDATE: I was able to compile the huge size of CHARMM by removing the options "-fdefault-integer-8 -frecord-marker" but still keeping "-mcmodel=medium".

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The "-frecord-marker=4" should have no effect on executable size, but may impact trajectory compatibility.


Rick Venable
computational chemist

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Originally Posted By: rmv
The "-frecord-marker=4" should have no effect on executable size, but may impact trajectory compatibility.

I tried to leave "-frecord-marker=4" in, but it did not compile.

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