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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Aug 03 2010 - 08:00:04 PDT
