On Tue, Mar 16, 2010, Taufik Al-Sarraj wrote:
>
> few of my simulations are failing at minimization. I tried the following.
> 1. turn SHAKE off in the second minimization step (the output below is
> from the second stage)
It looks like you and explicit water simulation (ntb=1). In such cases, you
cannot turn off SHAKE in any reliable fashion -- water models like TIP3p
(and protein models like Amber) have some atoms with zero Lennard-Jones
parameters, and these must be constrained via SHAKE in order for thing to work
well.
Amber does emphasize minimization for explicit water structures, primarily
because it is not a commonly used technique. If you have a bad starting
structure, doing some minimization to eliminate bad contacts can help, but
this is generally only a prelude to running molecular dynamics.
...good luck....dac
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Received on Tue Mar 16 2010 - 11:30:04 PDT
