AMBER Archive (2006)

Subject: AMBER: regarding diffusion command output

From: Arvind Marathe (arvind_at_mbu.iisc.ernet.in)
Date: Tue Aug 01 2006 - 05:45:21 CDT

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_at_P,O3',O5',C3',C4',C5'
diffusion :25-46 time 1.0 ions

go

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