Dear amber users,
I have done MD simulations on a DNA dodecamer with 22 Na+ counterions and
wanted to calculate their diffusion. So am using the diffusion command in
ptraj. Before using the diffusion command, am reimaging and also
rms-fitting to the first structure. In that case, my ions should not
diffuse more than the box-size. Is that correct? However if i calculate
square root of my ptraj outputs (which is diffusion squared) for several
ions from the file ions_r.xmgr, the diffusion values seem to touch 80 or
90 angstroms. However my box dimensions are only 48x48x64. So why is this
happening? Am i doing anything wrong?
Thanks and Regards,
Arvind
Follwing is the last part of my ptraj script:
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trajin A3T3_22.mdcrd.gz
trajin A3T3_23.mdcrd.gz
trajin A3T3_24.mdcrd.gz
trajin A3T3_25.mdcrd.gz
box x 48.000 y 48.000 z 64.000
center :1-12 mass origin
image origin center familiar
center :1-24 mass origin
image origin center familiar
rms first time 1.0 :1-24.P,O3',O5',C3',C4',C5'
diffusion :25-46 time 1.0 ions
go
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Received on Wed Aug 02 2006 - 06:07:11 PDT
