Can you try the following in the ptraj imaging?
--------- ptraj_imaging.in ------------
.(your trajin files)
.(your trajin files)
.(your trajin files)
image familiar com :(the first res of the protein)-(last res. of the protein)
---------------------------------------
What this will make is to make sure that the center-of-mass of the protein
will be at the origin. Hope this helps.
PS: I assume that you did not change the box info in the prmtop file.
> I am doing MD for a mouse ubiquitin, 1wgg, which has a long side chain. When
> I solvate the protein, I try solvateoct TIP3PBOX 12.0 and
> solvateoct TIP3PBOX 10.0. And I find out that the size of solute vdw
> bounding box is same: 36.162, 30.853, 52.074. So, I decide to use TIP3PBOX
> 10.0 since it has less water molecules.
>
> In the amber tutorial, it asks us to reimage all the water molecules into
> the original box. So I did it, and I find out that a very small part of my
> protein side chain drift into the vacuum after 1ns.
>
> However, if I don't reimage the water molecules into the original box, the
> whole protein is still in water. I am wondering whether or not my protein
> drifts out of water box. Do I trust the reimaged trajectory or the original
> trajectory?
>
> If my protein do drift out ot the water box, how do I fix it? I think I need
> to enlarge the water box, but both TIP3PBOX 12.0 and TIP3PBOX 10.0 give me
> the same size of water box. I know that if I don't truncate the waterbox, I
> won't have this problem. But I don't want to use so many water molecule in
> the simulation.
--
Ilyas Yildirim, Ph.D.
---------------------------------------------------------------
= Hutchison Hall B#10 - Department of Chemistry =
= - University of Rochester =
= 585-275-6766 (office) - =
= http://www.pas.rochester.edu/~yildirim/ =
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Received on Sun Sep 21 2008 - 05:08:55 PDT
