AMBER Archive (2007)

Subject: Re: AMBER: perturbed atoms are not bonded on using TIP5P water

From: Steven Winfield (saw44_at_cam.ac.uk)
Date: Fri Jan 12 2007 - 08:07:38 CST

Hi,

Do you need to turn on SHAKE?

Steve.

sugino tatsuro wrote:
> Greetings,
>
> Thanks for your quick reply very much.
>
> I created my system such that 1293 TIP5P waters were placed around a water
> molecule by using xLaep. Then I chose one of the water molecules to be
> perturbed.
> Only electric charge of atoms of the water molecule was perturbed into 0
> from default value.
> Bond information of perturbed water molecule could be confirmed by the
> command "desc" before saving topology and coordinate files.
> But there was no bond information in the saved topology file.
> So,when I performed MD simulation with these saved topology and coordinate
> files, perturbed atoms moved separately (because these are no bond).
>
> Thank you, with regards
> sugino
>
> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
> David A. Case
> Sent: Friday, January 12, 2007 7:12 AM
> To: amber_at_scripps.edu
> Subject: Re: AMBER: perturbed atoms are not bonded on using TIP5P water
>
>> On Thu, Jan 11, 2007, sugino tatsuro wrote:
>>> I'm going to perform thermodynamic integration using TIP5P model.
>>> The system I use is 3,000 water molecules, and the perturbed molecule is
> one
>>> of the waters.
>>> I successfully generated topology and coordinate files. But, in the
> topology
>>> file, the perturbed atoms are not bonded with other atoms. Namely, oxygen
>>> atom is not bonded with hydrogen atoms.
>
>> We need to know more about how you created the perturbed water: what does
> it
>> become in the perturbed state? What happens to the extra points that were
>> originally on the TIP5P model. How did you go about doing this?
>
>> ...dac
>
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