AMBER Archive (2003)

Subject: Re: AMBER: frozen x unfrozen

From: Herbert Georg (hcgeorg_at_if.usp.br)
Date: Thu Oct 23 2003 - 09:25:20 CDT

>
>
>>I would like to perform a simulation with a system in which one molecule
>>has to be flexible and the other has to be frozen (at least the bonds
>>have to be frozen). Is this possible??
>>I was reading about the keyword NTR and the group section but it's not
>>clear to me if the restraints are about the absolute positions of the
>>specified atoms or if its about their bonds.
>>
>>
>
>Ntr refers to the abosolute positions. I'm not sure what you mean when you
>say one molecule has to be "frozen". You could use ntr=1 to keep one molecule
>in a (nearly) fixed position and allow the other one to move.
>
>..good luck...dac
>
>
By frozen I mean that the molecule must have not internal degrees of
freedom (at least for bond lengths). While the other molecule must have
internal degrees of freedom.

>
>
>>Can I apply SHAKE to the molecule I want to keep frozen only?
>>
>>
>
>You can apply SHAKE to the part of the molecule that is also restrained by ntr
>restraints.
>
>..good luck...dac
>
>
>

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