AMBER Archive (2006)

Subject: Re: AMBER: about the execuation of REMD with sander of amber9

From: pang zhao (
Date: Sat Apr 29 2006 - 00:12:22 CDT

Sorry, I use the amber 9 not the amber 8 to perform remd. Now, I revised my

I use sander module of amber 9 to perform replica exchange MD. I just use 4
replicas to have a try. I just use single cpu to do it.
My commands:

sander -ng 4 -rem 1 -remlog remd.log -groupfile group &

the conten of file group:
-O -i mdin.rep1 -o mdout.rep1 -c min.restrt -p 1.prmtop -r re.rep1 -x
-O -i mdin.rep2 -o mdout.rep2 -c min.restrt -p 1.prmtop -r re.rep2 -x
-O -i mdin.rep3 -o mdout.rep3 -c min.restrt -p 1.prmtop -r re.rep3 -x
-O -i mdin.rep4 -o mdout.rep4 -c min.restrt -p 1.prmtop -r re.rep4 -x

The input of mdin.rep1 :
eplica Exchange MD
  ntwx = 100, ntpr = 100,
  ntt = 1, temp0 = 420.0, tempi = 0.0, tautp = 1.0,
  igb = 2,
  scnb = 2.0, scee = 1.2, dielc = 1, cut = 100.0,
  ntb = 0, ntc = 2, ntf = 2,
  nstlim = 5000, dt = 0.0020,
  ntp = 0,
  ibelly = 0, ntr = 0,
  imin = 0, irest = 0, ntx = 1,
  numexchg = 20, repcrd=1

However, the error arise: mdfil : Error: unknown flag -ng

in the amber 9 manual in page 166, the command is : $MPIRUN -np 16 sander
-ng 8 -groupfile groupfile

My command is similar to this.

When I type sander -h
the informatin arise:
sander [-help] [-O] [-A] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
[-ref refc -x mdcrd -v mdvel -e mden -idip inpdip -rdip rstdip -mdip mddip
-ng numgroup -remlog remlog -rem [0|1|2] -inf mdinfo -radii radii

I find there is no flag -groupfile,

By the way, the sander imformation is some different for the amber 9 manual
page 87:
sander [-help] [-O] [-A] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
-ref refc -x mdcrd -y inptraj -v mdvel -e mden -inf mdinfo -radii radii
-cpin cpin -cpout cpout -cprestrt cprestrt -evbin evbin

Please give me any suggestion how to tackle this problem. Great thanks

Best wishes

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