AMBER Archive (2006)

Subject: AMBER: Different results between serial and parallel runs in AMBER 8

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Mon Mar 06 2006 - 18:28:14 CST

Dear All,

I have a question on parallel and serial MD runs in AMBER 8. I have
created a system, which is a 4X4 base paired RNA, solvated in water. I
have created ordinary prmtop and inpcrd files. I compiled AMBER 8 both in
serial and parallel versions (renamed them as sander.serial and
sander.parallel). Then, I did a short run on this system, using
sander.serial and sander.parallel. Here are the first two step results:

--------------------------- parallel run -------------------------------
.
.
.
    10 fs simulation
     &cntrl
      imin=0,
      ntx=1,irest=0,
      ntpr=1,ntwr=1,ntwx=1,
      ntc=2,ntf=2,ntb=1,cut=8,
      igb=0,
      ntr=0,
      nstlim=10,dt=0.001,nscm=5000,nrespa=1,
      ntt=3,gamma_ln=1,tempi=300,temp0=300,ig=233,
      ntp=0,taup=2.0,pres0=1
     /
.
.
.
 NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 439.42 PRESS = 0.0
 Etot = 4337.6493 EKtot = 6803.5776 EPtot = -2465.9282
 BOND = 66.7991 ANGLE = 128.2466 DIHED = 205.4474
 1-4 NB = 74.6955 1-4 EEL = -1233.7386 VDWAALS = 100.1044
 EELEC = -1807.4827 EHBOND = 0.0000 RESTRAINT = 0.0000
 Ewald error estimate: 0.1351E-02
 ------------------------------------------------------------------------
 NSTEP = 1 TIME(PS) = 0.001 TEMP(K) = 345.43 PRESS = 0.0
 Etot = 2882.4294 EKtot = 5348.3577 EPtot = -2465.9282
 BOND = 66.7991 ANGLE = 128.2466 DIHED = 205.4474
 1-4 NB = 74.6955 1-4 EEL = -1233.7386 VDWAALS = 100.1044
 EELEC = -1807.4827 EHBOND = 0.0000 RESTRAINT = 0.0000
 Ewald error estimate: 0.1351E-02
.
.
.
-------------------------------------------------------------------------

------------------------------ serial run -------------------------------
.
.
.
    10 fs simulation
     &cntrl
      imin=0,
      ntx=1,irest=0,
      ntpr=1,ntwr=1,ntwx=1,
      ntc=2,ntf=2,ntb=1,cut=8,
      igb=0,
      ntr=0,
      nstlim=10,dt=0.001,nscm=5000,nrespa=1,
      ntt=3,gamma_ln=1,tempi=300,temp0=300,ig=233,
      ntp=0,taup=2.0,pres0=1
     /
.
.
.
 NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 439.42 PRESS = 0.0
 Etot = 4337.6493 EKtot = 6803.5776 EPtot = -2465.9282
 BOND = 66.7991 ANGLE = 128.2466 DIHED = 205.4474
 1-4 NB = 74.6955 1-4 EEL = -1233.7386 VDWAALS = 100.1044
 EELEC = -1807.4827 EHBOND = 0.0000 RESTRAINT = 0.0000
 Ewald error estimate: 0.1351E-02
-------------------------------------------------------------------------
 NSTEP = 1 TIME(PS) = 0.001 TEMP(K) = 332.09 PRESS = 0.0
 Etot = 2675.8869 EKtot = 5141.8152 EPtot = -2465.9282
 BOND = 66.7991 ANGLE = 128.2466 DIHED = 205.4474
 1-4 NB = 74.6955 1-4 EEL = -1233.7386 VDWAALS = 100.1044
 EELEC = -1807.4827 EHBOND = 0.0000 RESTRAINT = 0.0000
 Ewald error estimate: 0.1351E-02
.
.
.
-------------------------------------------------------------------------

I have used the same md.in file. In the above results, the NSTEP = 0 have
the same values (which is expected because the structures are exactly the
same). But when it becomes NSTEP = 1, the temp. values changes; in one
case it is 345.43 and in the other case it is 332.09. And as a result, the
rest of the NSTEPs have different values when serial and parallel runs are
compared. Is this an expected behavior?

Best, 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
  ---------------------------------------------------------------

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu