AMBER Archive (2006)

Subject: Re: AMBER: center molecule using iwrap=1?

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Thu Jul 13 2006 - 14:43:37 CDT

then I think using ptraj to center the peptide and image the water
for each frame should be ok.

Gustavo Seabra wrote:

> Well, I want, for exemple, to locate all water molecules within some
> distance from the peptide, using for example a VMD script. If the
> molecule is close to the edge of the box, then the script gets more
> complicated (although it's not impossible...)
>
> Thanks,
>
> Gustavo.
>
> On 7/13/06, Carlos Simmerling <carlos_at_csb.sunysb.edu> wrote:
>
>> you could use a positional restraint on one or more atoms
>> to keep the peptide in the center but I would worry about the
>> effect on the dynamics. I would think it would be better to let
>> it drift and then use ptraj to center it, then do your analysis on
>> that trajectory. it's hard to really say much more since you don't
>> say why your analysis will need it centered.
>>
>> Gustavo Seabra wrote:
>>
>> > Hi All,
>> >
>> > I have a system of a small peptide in explicit water.
>> >
>> > I know that, using ptraj, I can put the peptide inthe center of the
>> > box and wrap all waters around it, so as to create a new crd file with
>> > my molecule always in the center of the box and wrapping the waters
>> > around it.
>> >
>> > I wonder if something like it is possible by using iwrap=1 instead. I
>> > mean, define it to wrap the molecules, (iwrap=1) AND keep the peptide
>> > in the center od the box. Is that possible? How?
>> >
>> > (I'm worried that just with iwrap=1 alone the peptide will be allowed
>> > to drift inside the box. Although it has no effect on the dynamics, it
>> > will change the analysis I want to do later.)
>> >
>> > Thanks a lot!
>
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