Dear Carlos,
Thank you for your reply. I used VMD (which has some pbc wrap tools) to wrap
the trajectory and as I compared it with that after I used ptraj, they are
completely different, that's why I am wondering if I did something wrong or
it's because of the box I used.
I have another small question, I used ptraj to wrap the box as following:
trajin md1_6th.mdcrd.gz
trajin md2_6th.mdcrd.gz
trajin md3_6th.mdcrd.gz
trajin md4_6th.mdcrd.gz
trajin md5_6th.mdcrd.gz
trajout reimage_md1to5_6th.mdcrd.gz
center
image familiar
go
What I want to ask is will it change the trajectories if I used center for
all the atoms, or if I used center for only the atoms in the protein, like:
trajin md1_6th.mdcrd.gz
trajin md2_6th.mdcrd.gz
trajin md3_6th.mdcrd.gz
trajin md4_6th.mdcrd.gz
trajin md5_6th.mdcrd.gz
trajout reimage_md1to5_6th.mdcrd.gz
center : 1-5668
image familiar
go
Thank you for your answer.
Rachel
On 7/26/07, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
>
> if you wrap in ptraj there's really no way to wrap to a rectangular
> box- and if you did, some molecules may overlap. you should
> wrap back to the same box used in the MD unless you really know
> what you're doing (and can go through the extra steps you would need)
>
> On 7/26/07, Rachel <comeonsos.googlemail.com> wrote:
> > Dear all,
> >
> > I solvated my protein with truncated octahedral water box, and the iwrap
> is
> > set to 0, and I want to image the trajectory back to primary box for
> > analysis, can I ask if I used a rectangular box rather than a truncated
> > octahedral box to wrap the trajecotries, will that change the
> trajectories
> > or the results would still be the same? thank you.
> >
> > Kind regards,
> > Rachel
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Received on Sun Jul 29 2007 - 06:07:25 PDT
