AMBER Archive (2008)

Subject: AMBER: ptraj & imaging of velocities

From: FyD (
Date: Tue Sep 02 2008 - 08:06:08 CDT

Dear Amber users,

We got **** characters in a restrt file (MD simulation carried out
using iwrap=0; Amber 8); consequently our MD simulation crashed. This
problem has been already reported in the Amber mailing list. As we
save restrt files each nsec, we used a previous restrt file (without
**** characters) to re-image the corresponding Cartesian coordinates
using ptraj (& to re-run the MD simulation using ntx = 5, irest = 1).
However, in this case the velocities are set to zero by ptraj...

Is it correct to re-image the velocities (derivative) as we re-image
the Cartesian coordinates using ptraj ? (in this case, we have to
change the order Cartesian coordinates - velocities in the restrt
file; see below)

Thank you, regards, Francois

Step 1:
"restrt-a1" ----> "restrt-b"
Cart. coord re-imaged Cart. coord
velocities set to zero: do not use them

Step 2:
"restrt-a2" ----> "restrt-c"
velocities (*) re-imaged velocities
Cart. coord set to zero: do not use them

(*) manually change the order "Cart. coord" <--> "velocity" in the restrt file

Step 3:
"restrt-b" manually
                ---> "restrt-d"
"restrt-c" re-imaged "Cart. coord + velocities"

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