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:
ptraj
"restrt-a1" ----> "restrt-b"
Cart. coord re-imaged Cart. coord
velocities set to zero: do not use them
Step 2:
ptraj
"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"
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Wed Sep 03 2008 - 06:07:47 PDT
