AMBER Archive (2007)

Subject: Re: AMBER: Rotations about center of mass of an isolated system

From: Jennie Thomas (jenniet_at_uci.edu)
Date: Mon May 14 2007 - 14:50:30 CDT

Yes, I get the message in the output file, but it appears no
translations or rotations are removed. It is clear from looking at a
movie of the trajectory that there are collective rotations of the
atoms. Here is an example of the message in the output file:

check COM velocity, temp: 0.000000 0.00(Removed)
check COM velocity, temp: 0.000000 0.00(Removed)
check COM velocity, temp: 0.000000 0.00(Removed)
check COM velocity, temp: 0.000000 0.00(Removed)
check COM velocity, temp: 0.000000 0.00(Removed)
check COM velocity, temp: 0.000000 0.00(Removed)
check COM velocity, temp: 0.000000 0.00(Removed)
check COM velocity, temp: 0.000000 0.00(Removed)
check COM velocity, temp: 0.000000 0.00(Removed)
check COM velocity, temp: 0.000000 0.00(Removed)
check COM velocity, temp: 0.000000 0.00(Removed)
check COM velocity, temp: 0.000000 0.00(Removed)
check COM velocity, temp: 0.000000 0.00(Removed)
check COM velocity, temp: 0.000000 0.00(Removed)
check COM velocity, temp: 0.000000 0.00(Removed)

After the first step there is a slight correction:

check COM velocity, temp: 0.029286 1.39(Removed)

The temperature fluctuates around 250 K, which seems normal. I've
equilibrated the system in NPT and experienced the same issue with
lack of removal of rotations.

Any further advice or ideas?

Thanks,
Jennie

On May 14, 2007, at 9:19 AM, David A. Case wrote:

> On Thu, May 10, 2007, Jennie Thomas wrote:
>>
>> I'm running an isolated small water cluster using Amber 8 (NVE
>> ensemble). The cluster is rotating about the center of mass during
>> the simulation run. I've tried to play with NSCM to remove both
>> rotations and translations from the dynamics. But, there is still a
>> collective rotational motion even setting NSCM=1. Any ideas why the
>> collective rotations aren't being removed from the dynamics?
>
> Do you get messages in the output about removal of translation and
> rotation?
> Do these show very high energies or temperatures? If the water
> cluster
> is fluxional, so that there is no average structure, it is
> certainly possible
> that removing the instantaneous rotation about the current
> structure may not
> do what you want. How are you deicding that collective rotations
> are not
> being removed?
>
> ...regards...dac
>
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