Dear users,
I am trying to set up a system for steered MD in amber14. the solute RNA
is oriented along z axis and for pulling simulations i need an elongated
water box in z direction. From some post in the mailing list, i tried this
command:
solvatebox mol TIP3PBOX {30 30 45}
Although it works, but the generated water molecules overlap with solute
atoms and the bad contacts persist even after minimization and
equilibration process (checkoverlap command gives a lot of bad contacts in
the box)
Is this a correct way to generate asymmetric box or is there any other way
to do it?
Thanks
Asmita
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Apr 23 2015 - 11:00:04 PDT
