Hello Thomas
Thank you so much for your reply.
For the force field, I am using GAFF and AM1/BCC charge method. I followed
exactly the method introduced in the tutorial in the official website to
prepare the prmtop file.
As for the simulation runs, I used the default setting of iwrap, which is
iwrap=0 in my recall.
The animation that I created was using the raw trajectory under this
condition. If the water is present, they would disperse very far away from
the polymer.
Even after I used "image" command to post-process the raw trajectory, that
kind of funny motion of polymer remains.
And I am not sure whether the drastic change of the polymer motion is due to
ill-defined potential, because it requires very intensive force to deform
the solute in that kind of short time. Furthermore, if that kind of
extensive force exists, the polymer should explode at that instant. Just an
instinct argument.
I will try as you said.
Thank you very much. You suggestion is highly appreciated.
Best!
Bin
2011/8/25 Thomas Cheatham III <tec3.utah.edu>
>
> > By random rotation, I mean the rotation that I observed happens too quick
> to
> > be true. In my opinion, the time scale of the rotation should be around 1
> ns
> > or more. But the rotation in my case just happen within a couple of 100
> fs.
> > Please check the animation from links in my very first mail.
>
> The animations are not clear to me and I cannot tell what processing you
> have done to obtain the images. If it is an imaging issue, you should see
> molecules moving outside the periodic box or abruptly translating (the box
> length) not rotations.
>
> If the polymer is one single molecule (i.e. residues 1-125) then it is
> definately not an imaging issue (since molecules are imaged intact).
>
> I would run the trajectory with IWRAP=0 dumping out every step (NTWX = 1)
> or every 5 steps in a (short) 5 ps run (since you claim you are seeing
> funny motion on 100 fs time scale). If in the continuous dynamics you see
> funny stuff, this is probably a force field issue with your polymer and
> not an imaging issue.
>
> With IWRAP=0 if molecules are moving out of the box you will see
> molecules continuously move further and further from the central box. If
> so, this is potentially imaging. If not, then it has nothing to do with
> RMS or IMAGE.
>
> I would look at a movie of the chain of carbon atoms (with the water
> hidden) or a movie of a subset of the polymer. If you dump every frame,
> you should not see abrupt motions (except via box translations, however,
> these will be absent with IWRAP=0).
>
> --tec3
>
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Received on Thu Aug 25 2011 - 14:30:03 PDT
