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.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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-------------------------------------------------
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.univ-paris-diderot.fr
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Received on Mon Mar 02 2009 - 01:08:12 PST
