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/ -
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Received on Sun Mar 12 2006 - 06:10:10 PST
