Dear Amber,
I am using Amber10. I have been simulating my system for long time
scales (more than 45 ns) with iwrap=0. I get *** printed in my restart
file for such a long time scales and pmemd gets killed stating that it
cannot read coordinates from previous restart file. I understand that this
is only due to the format of restart file (6f12.7) that amber follows.
This format allows any atom's coordinates to be in the range -999.9999999
to 9999.9999999 A. For long simulations, it was suggested that one should
use iwrap = 1 but at the cost of diffuse properties of the system.
My question is, if I want to avoid iwrap=1 and use restart file format to
be 6f12.6, is there any practical issue with simulation? This would allow
any atoms's coordinate to be in the range -9999.999999 to 99999.999999. Is
the 7th decimal matters so much in restarting simulation? Note that
trajectory file has (I think) 10f8.3 format and has no problem since it
is not used to restart any simulation.
On the otherhand, suppose that after a long simulation (before coord reach
6f12.7 limit) I image my system using ptraj with respect to my center
molecule. Here ptraj wont preserve the velocities and hence I manually
keep the velocities to the imaged restart file and do the usual pmemd
with again iwrap=0. Am I doing anything against physics here?
Thanks and regards,
Santosh.
--
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Apr 26 2011 - 00:00:02 PDT
