Hi,
You imaged with respect to your whole solute(:1-20) not the residue 1(:1).
This means that residue 1 is not always in the center. In this case, if you
specify 'noimage', some of the distances between a solvent molecule and
residue 1 can be farther than the distances calculated without 'noimage'.
On Tue, Aug 3, 2010 at 10:30 AM, Xioling Chuang <xioling_c.hotmail.com>wrote:
>
> Dear All,
>
>
>
> I am using amber9 and tried to perform MD simulation of polyAT 10-mer.
> After MD simulation, I used ptraj to shift molecules back into the primary
> unit cell using the following script
>
> ----------------------->
>
> trajin polyAT.mdcrd
>
> trajout polyAT.trj
>
> center :1-10 mass origin
>
> image origin center
>
> center :1-20 mass origin
>
> image origin center
>
> go
>
> <-----------------------
>
>
>
> Then I tried to calculate the distance between Na+ ions and some residue,
> e.g. residue#1, using two different script files (with/wothout option
> noimage), as below;
>
>
>
> "dist1.in"
>
> ------------------------------>
>
> trajin polyAT.trj
>
> distance jj1 :21 :1 out dist1.Na1.dat
>
> distance jj2 :22 :1 out dist1.Na2.dat
>
> distance jj3 :23 :1 out dist1.Na3.dat
>
> distance jj4 :24 :1 out dist1.Na4.dat
>
> go
>
> <-----------------------------
>
>
>
> "dist2.in"
>
> ------------------------------>
>
> trajin polyAT.trj
>
> distance jj1 :21 :1 out dist2.Na1.dat noimage
>
> distance jj2 :22 :1 out dist2.Na2.dat noimage
>
> distance jj3 :23 :1 out dist2.Na3.dat noimage
>
> distance jj4 :24 :1 out dist2.Na4.dat noimage
>
> go
>
> <------------------------------
>
>
>
> I expected that I should obtained the same results, since the trajectory
> file "polyAT.trj" was already imaged. However, the obtained results were
> that some outputs are the same, e.g. the distances of all snapshots in
> "dist1.Na1.dat" & "dist2.Na1.dat", but some are not the same, e.g. all
> distances in "dist2.Na3.dat" are ~5 Angstrom larger than those in
> "dist1.Na3.dat". This seems to me that some ions were not properly imaged
> when we used command "image origin center". Or is there any mistake for my
> script file? Any suggestion?
>
>
>
> One more question, is it possible to calculate the distance between each
> Na+ ions and residue#1 using one command line and how? or should I use 18
> command lines of 18 Na+ ions?
>
>
>
> Thank you very much in advance for your kindness.
>
> Best,
>
> Xioling
>
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Best,
InSuk Joung
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Received on Tue Aug 03 2010 - 08:30:11 PDT
