Hello:
I am running NVT with following .in file by GPU acceleration
heating gradually over 600ps
&cntrl
imin=0,irest=0,ntx=1,
nstlim=600000,dt=0.001,
ntc=2,ntf=2,
cut=9.0, ntb=1,
ntpr=500, ntwx=500,
ntt=3, gamma_ln=2.0,
tempi=0.0, temp0=300.0,
restraintmask=':1-291 &!.H,WAT &.O',
restraint_wt=6.0,
iwrap=1,
nmropt=1
/
&wt TYPE='TEMP0', istep1=0, istep2=600000,
value1=0.1, value2=300.0, /
&wt TYPE='END' /
with command:
mpirun -n 2 pmemd.cuda.MPI -O -p sys.prmtop -c mini-05.rst7 -ref
mini-05.rst7 -i nvt.in -o nvt.out -x nvt.trj -inf nvt.info -r nvt.rst7
my jobs always stacked with following nvt.out log file after hours of
running:
4. RESULTS
--------------------------------------------------------------------------------
---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
---------------------------------------------------
|---------------------------------------------------
| APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.39
| APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.84
|---------------------------------------------------
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS
= 0.0
Etot = -154386.9735 EKtot = 0.0000 EPtot =
-154386.9735
BOND = 151.7050 ANGLE = 751.2505 DIHED = 4836.7085
1-4 NB = 954.6833 1-4 EEL = 12018.0185 VDWAALS = 26886.9444
EELEC = -199986.2836 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
I don't observe any complain or errors in the job running. Does anyone
have any advices? My workstation have two GTX590.
thank you very much
best
Albert
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Received on Mon Mar 18 2013 - 09:00:02 PDT
