Hi Mingfeng:
Then the problem may come from the ptraj part. Blow is the ptraj script
I used for the trajectory. Water is striped except those in active site.
Residue 1-316 is from protein. Do you know what is wrong?
reference ycd.inpcrd
trajin md_npt2.crd.gz
rms reference out rms-ycd-cry-320k .CA
center .CA
image center
strip ~:1-316,1091,5345,5702,5902,6376,8799,9524,10065,12061,12382,15338
trajout md_npt2_waterpath.crd
go
Best,
Lishan
On Thu, 2005-10-27 at 12:11, Mingfeng Yang wrote:
> According to my understanding, they could be, but not neccessary.
> Because you save your snapshot into a trajectory file every ntwx steps,
> in your case, if 500,000/ntwx = an integar, then they are the same,
> otherwise, no.
>
> If I am wrong, somebody please correct me.
>
> Mingfeng
>
> Lishan Yao wrote:
>
> >Dear Amber users:
> > I did a 500,000 steps MD simulation and I saved snapshots every 1000
> >steps. My question is whether the restart file and the last snapshot in
> >crd (trajectory) file has the same structure? The reason I ask this
> >question is that I found out water molecules in active site have
> >different positions in the two structures.
> >
> > Thank you in advance.
> >
> >Best,
> >Lishan
> >
> >
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Received on Thu Oct 27 2005 - 18:53:01 PDT
