AMBER Archive (2006)

Subject: AMBER: Replica exchange with Amber9

From: Atsutoshi Okabe (okabe_at_cherry.bio.titech.ac.jp)
Date: Fri Jul 14 2006 - 01:20:21 CDT

Dear all

 

I perfomed replica exchage MD with Amber8 and Amber9 , Both systems are
quite same.

The calculation successed when I used Amber8 but not when I used Amber9. I
think this is very strange.

 

Then when I used Amber9 , I've got the following error message.

 

     Coordinate resetting (SHAKE) cannot be accomplished,

     deviation is too large

     NITER, NIT, LL, I and J are : 0 1 153 315 317

 

     Note: This is usually a symptom of some deeper

     problem with the energetics of the system.

 

Why did I get the error message and stop calculation only when I used
Amber9?

 

This is my sander script with Amber9.

 sander.MPI -ng 16 -rem 1 -remlog rem.log -groupfile groupfile"

 

And my groupfile is

-O -i REM.in.000 -p INIT.top -o REM.out.000 -c md.rst.000 -r REM.rst.000 -x
REM.trj.000

-O -i REM.in.001 -p INIT.top -o REM.out.001 -c md.rst.001 -r REM.rst.001 -x
REM.trj.001

 

I set REM.in.000 file the following.

&cntrl

  ntx=5, irest=1,

  ntf=2, ntc=2,

  ntt=1,

  ntb=0, igb=2, saltcon=0.2, gbsa=1,

  cut=15.0,

  tempi=270, temp0=270,

  dt=0.002, nstlim=200,

  ntpr=100,ntwx=100,ntwr=100,

  numexchg=2250,

 

Could you please give me any suggestions?

 

Atsutoshi

 

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