Re: Speeding up: Dummy constructions for aromatics or hydrogens

From: DimitryASuplatov (genesup_at_gmail.com)
Date: Fri Apr 17 2009 - 15:50:03 CDT

Thank you for answering.

>> I`ve been using gromacs previously. It is generaly a default strategy in
>> gmx to use dummy constructions for hydrogens or aromatics and heavy
>> hydrogens constructions. This enables fast and reliable calculations
>> with up to 4fs.
>
> hmm... "constructions" sounds strange. i have not seen
> this in the gromacs documentation, either.
> are you talking about "constraints"?
>

I meant "dummy atoms" for aromatics or hydrogens. It is -vsite
aromatics/hydrogens option for pdb2gmx.
Is it the same as "rigidBonds" in namd?

Thanks

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