AMBER Archive (2009)

Subject: [AMBER] binding free energy

From: Maryam Hamzehee (maryam_h_7860_at_yahoo.com)
Date: Sun Mar 01 2009 - 05:52:43 CST

Dear All
I am trying to run a simulation (20 ns) in order to calculate the binding free energy for the association of two proteins, I used the following script :
 
mpirun -np 32 /opt/pmemd -O -i prod.in -o prod1.out \ -p egf-egfr_solvated.prmtop -c equil.rst -r prod1.rst -x prod1.mdcrd
mpirun -np 32 /opt/pmemd -O -i prod.in -o prod2.out \ -p egf-egfr_solvated.prmtop -c prod1.rst -r prod2.rst -x prod2.mdcrd
mpirun -np 32 /opt/pmemd -O -i prod.in -o prod3.out \ -p egf-egfr_solvated.prmtop -c prod2.rst -r prod3.rst -x prod3.mdcrd
mpirun -np 32 /opt/pmemd -O -i prod.in -o prod4.out \ -p egf-egfr_solvated.prmtop -c prod3.rst -r prod4.rst -x prod4.mdcrd
gzip -9 prod*.mdcrd
 
And here is the prod.in file:
heat egf-egfr
 &cntrl
  imin=0,irest=1,ntx=5,
  nstlim=2500000,dt=0.002,
  ntc=2,ntf=2,
  cut=8.0, ntb=2, ntp=1, taup=2.0,
  ntpr=5000, ntwx=5000,
  ntt=3, gamma_ln=2.0,
  temp0=300.0,
 /

 
Suddenly the program stopped due to unclear reason; files related to prod3.out  prod3.mdcrd produced not completely and prod3.rst has nothing in its content.
 
Content of mdinfo file is shown below,
 
 NSTEP =  1410000   TIME(PS) =    8420.000  TEMP(K) =   299.33  PRESS =  -142.8
 Etot   =   -201727.2431  EKtot   =     50187.6389  EPtot      =   -251914.8820
 BOND   =      1708.3109  ANGLE   =      4472.5447  DIHED      =      5210.6720
 1-4 NB =      1946.4847  1-4 EEL =     22570.1132  VDWAALS    =     29543.6234
 EELEC  =   -317366.6309  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 EKCMT  =     22003.9326  VIRIAL  =     24529.5547  VOLUME     =    819084.0618
                                                    Density    =         1.0226
 Ewald error estimate:   0.4641E-04
 
It seems that simulation has been done up to 8.4 ns, How can I continue my simulation up to 20 ns.
 
Any help in this regard would be highly appreciated,
 
All the best,
Maryam
 
 

      
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