Dear Amber Users,
I am analyzing the MD trajectory of Amber. I would like to calculate how
many atoms of solvent molecules are in contact with each amino acid
residue. For this reason I wrote a small Tcl script in VMD which can
calculate contact of each residue with solvent molecules within 3.5 Ang.
My question is I did NPT MD in Amber 10. In trajectory solvent molecules
gets spread out in the space outside the box. When I do reimaging the
atoms are placed back in the box. I am not sure which trajectory should
I take to calculate the contact of solvent molecule.
Is it that while reimaging the trajectory, the dynamics of motion is
affect. I mean if in the original simulation the atoms flying around all
the places under the spell of forcefield; won't the forces, and energies
would be different, if I put them artificially in the box, while
reimaging?
Hope to hear from Amber users.
Thanks a lot
Abdul Rajjak
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Received on Fri Feb 05 2010 - 02:30:06 PST
