AMBER Archive (2009)

Subject: Re: [AMBER] binding free energy

From: Barbault Florent (florent.barbault_at_univ-paris-diderot.fr)
Date: Sun Mar 01 2009 - 06:20:39 CST

Hello,

Simple question: Do you have enough free space on your hard drive? It
happened to me and gave me this sort of stop.

Regards
Florent Barbault

I On Sun, 1 Mar 2009 03:52:43 -0800 (PST)
  Maryam Hamzehee <maryam_h_7860_at_yahoo.com> wrote:
> 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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> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

-------------------------------------------------
Dr Florent Barbault
Maitre de conferences / Assistant professor

NEW ADDRESS !!!

Universite Paris Diderot
Laboratoire ITODYS
15 rue Jean de Baïf, bâtiment Lavoisier
75013 Paris FRANCE
http://www.itodys.univ-paris7.fr/
tel : (33) 01-57-27-88-50
e-mail : florent.barbault_at_univ-paris-diderot.fr
-------------------------------------------------

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