AMBER Archive (2005)

Subject: AMBER: unstable MD velocities

From: hayden (s0237717_at_sms.ed.ac.uk)
Date: Thu Sep 01 2005 - 12:38:11 CDT

Dear Amber users

I have created a lipid chain bound to 2 carbohydrate moieties using gaff
parameters. The partial charges were generated using a gaussian/resp
procedure.

The problem is this:

Dynamics runs of the molecule (in gas phase and igb=1) rapidly give rise to
huge velocities that quickly cause the system to crash. The crash can only
be avoided by resetting the velocities after every dynamics cycle.

I have tried varying the ntt setting but this has not helped. I presume that
there must be some parameter conflict within my molecule?

Any help would be very much appreciated.

I have included my dynamics input file and the parm and crd files.

Many thanks

______________________________________________
Hayden Eastwood
Perdita Barran Research Group
Joseph Black Building
Edinburgh University
West Mains Road
EH9 3JJ
 
Tel: 0131 650 4773
e-mail: s0237717_at_sms.ed.ac.uk
Research page:http://homepages.ed.ac.uk/pbarran/PBRG/
"You have to be an academic to believe some things; no ordinary person would
be so stupid." -George Orwell



  • application/octet-stream attachment: prm.top

  • application/octet-stream attachment: md.in

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