From: Prem Raj Joseph <>
Date: Wed 08 Mar 2000 11:20:16 +0000


I am prem raj. I am carrying out some molecular dynamics simulation on a
modifies DNA duplex using particle mesh ewald method with explicit ions and
water. I have position the ions at a distance of 5A along the bisector of
angles of O1P--P--O2P using the CION option and placed the solute in TiP3P
water using the BOX option.

During the initial equilibration runs of minimisation and molecular dynamics
, I find the ions moving away too much from the solute ( say 10 to 15 A).
This seems to be bit unusual.

Regarding the modifies DNA duplex.

The DNA I am working on has a 2',5' phosphodiester linkage rather than than
the naturally occuring 3',5' linked DNA.

To prepare the data base for the modified DNA. I have made a few changes in
the prep input as compared to the 3',5' ones available in

1) My main chain is as follows

P-- O5'-- C5'-- C4'-- C3'--C2'-- O2'-- P and the poential types are
P-- OS -- CT -- CT -- CT -- CT -- OS -- P and the tree is as below
M -- M -- M -- M -- M -- M -- M -- M

2) I have made the following changes with the charges

Dut to the change in the linkage I have swaped the charges on
C2', O2' with that of C3', O3' atoms respectively ( an given in
   and vis versa.
Also the charges on the hydrogens H2' is replaced with that of H3'
and the charges on H3'1 and H3'2 is replaced with that of H2'1 and H2'2
Thus the total charge on the residues is maintained the same.

Could this change in the charges introdued be the culprit for the unusual
movement of the ions from the solute.

thanking you

prem raj

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Received on Wed Mar 08 2000 - 03:20:16 PST
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