Re: [AMBER] Freezing atoms in space during a simulation

From: Jonathan Gough <>
Date: Wed, 17 Jun 2015 06:22:54 -0700 (PDT)

Thank you all for your help!

Ibelly  is only in the cpu code. The calculation is up and running.  Great reminder of how spoiled we are with the gpu code! (Thanks Ross, Scott, and everyone else! )

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On Tue, Jun 16, 2015 at 4:39 PM, Gustavo Seabra <>

> On ter jun 16 2015 17:19:00 David A Case said:
>> On Tue, Jun 16, 2015, Jonathan Gough wrote:
>>> Is there a way to hold several atoms fixed during a simulation.
>> See the "ibelly" option, section 18.6.4 in the 2015 Amber Reference Manual.
> Notice that in “ibelly” you specify the atoms that will be allowed to move. You would need a mask that can select every atom in the system *but* the ones you want fixed. Depending on your system, it may be easier to just change the code directly.
> Gustavo.
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Received on Wed Jun 17 2015 - 06:30:03 PDT
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