AMBER Archive (2004)

Subject: AMBER: Moil-view & Amber trajectory

From: opitz_at_che.udel.edu
Date: Fri Sep 17 2004 - 15:41:42 CDT

('binary' encoding is not supported, stored as-is) Dear Amber community,

I ran a simulation with the following input in Amber7:

&cntrl
        imin=0, irest=1, ntx=5,
        iwrap=1,
        ntb=2, ntp=1, pres0=1.013, taup=2.0,
        ntf=1,
        igb=0,
        ntr=0, cut=12,
        ntt=1, tempi=300.0, temp0=300.0, tautp=1.0,
        nstlim=30000, dt=0.001, t=20,
        ntpr=100, ntwx=100, ntwr=1000
&end

When the run is done, I combine the trajectory of this and a run before
and after it using ptraj. The run before this had the solute restrained
as it is outlined in the amber tutorial online.
When viewing the trajectory as it progresses through time in moil-view
(version 10.1) the molecules are all over the place, in the sense that
the bonds are way too long.
In ptraj I tried to just combine the trajectories (with and without the
fixed solute run). Then I tried the image function (although it shouldn't
be necessary, with iwrap=1, right?), still the same result.
Why does moil-view, when viewing the trajectory (while it is making the
movie), show such long bonds, instead of the right bonds of individual
solvent and solute molecules?

Best Regards,

Armin

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