AMBER Archive (2008)

Subject: AMBER: replica exchange with amber9

From: greddy1_at_umd.edu
Date: Tue Sep 23 2008 - 17:44:24 CDT

Hello all,
I am relatively new to AMBER. I have used the tutorials which are excellent to get
myself acquainted with the software. Right now I am trying to do a replica
exchange simulation of a peptide using amber9. I am running into problems.
The simulation stops after the first exchange. I have used the tutorial on the
Amber web page for replica exchange which is for version 10. Probably, this is
causing some problems. Can any one help me figure out the problem or point
me to a tutorial for replica exchange using amber9.
Thanks
Greddy

My input script for the tutorial:

pep replica exchange simulation
 &cntrl
  irest=0, ntx=1,
  nstlim=5000, dt=0.002,
  irest=0, ntt=3, gamma_ln=1.0,
  temp0=XXXXX, ig=RANDOM_NUMBER,
  ntc=2, ntf=2, nscm=1000,
  ntb=0, igb=5,
  cut=12.0,
  ntpr=5000, ntwx=5000, ntwr=5000,
  nmropt=1,
  numexchg=2500
 /
 &wt TYPE= END
 /
DISANG=pep_cap_amber_chir.dat
*****************************************************
Log file output:

# replica exchange log file
# numexchg is 2500
# Replica #, Velocity Scaling, T, Eptot, Temp0, NewTemp0, Success rate (i,i+1)
# exchange 1
 1 -1.00 0.00 -697.55 270.00 270.00 0.00
 2 -1.00 0.00 -724.27 281.32 281.32 0.00
 3 -1.00 0.00 -711.78 293.12 293.12 0.00
 4 -1.00 0.00 -660.99 305.41 305.41 0.00
 5 -1.00 0.00 -613.79 318.22 318.22 0.00
 6 -1.00 0.00 -618.67 331.56 331.56 0.00
 7 -1.00 0.00 -594.27 345.47 345.47 0.00
 8 1.02 0.00 -538.81 359.95 375.05 2.00
 9 0.98 0.00 -565.57 375.05 359.95 0.00
10 -1.00 0.00 -470.63 390.78 390.78 0.00
11 -1.00 0.00 -446.30 407.16 407.16 0.00
12 -1.00 0.00 -441.40 424.24 424.24 0.00
13 -1.00 0.00 -375.77 442.03 442.03 0.00
14 -1.00 0.00 -410.95 460.56 460.56 0.00
15 -1.00 0.00 -370.95 479.88 479.88 0.00
16 -1.00 0.00 -353.13 500.00 500.00 0.00
****************************************************************
Result part of the output for one of the replicas:
-------------------------------------------------------------
-------------------
   4. RESULTS
-------------------------------------------------------------
-------------------

 NSTEP = 0 TIME(PS) = 5000.000 TEMP(K) = 0.00 PRESS = 0.0
 Etot = -697.5475 EKtot = 0.0000 EPtot = -697.5475
 BOND = 94.0549 ANGLE = 227.8215 DIHED = 178.6298
 1-4 NB = 104.4641 1-4 EEL = 1802.5777 VDWAALS = -170.8794
 EELEC = -2354.0564 EGB = -580.4516 RESTRAINT = 0.2922
 EAMBER (non-restraint) = -697.8396
 -------------------------------------------------------------
-----------------

 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.292
=================================================
==============================
 Exiting runmd after getting initial energies for REMD 0

***************************************************************
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu