hello:
I am using the following command and input file to run NPT
*mpiexec -np 2 $AMBERHOME/bin/pmemd.cuda.MPI -O -p apo.prmtop -c m6.rst
-ref m6.rst -i npt1.in -o npt1.out -r npt1.rst -x npt1.mdcrd -inf npt1.info*
*
*
*equilibration*
* &cntrl*
* imin=0, irest=0, ntx=1,*
* nstlim=500000, dt=0.002,*
* ntc=2, ntf=2,*
* cut=10.0, *
* ntb=2, ntp=3, taup=2.0, pres0=1,*
* ntpr=5000, ntwx=5000, ntwr=50000,*
* ntt=3, gamma_ln=1.0, ig=-1,*
* iwrap=1,*
* temp0=310.0,*
* csurften=3, ninterface=2, gamma_ten=17,*
* restraintmask='1-396 &!.H',*
* restraint_wt=20,*
* /*
however, I found that the npt1.out and npt1.info stacked there after
several hours of running:
*
*
* ---------------------------------------------------*
* 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. 2.33*
*| APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION*
*| with 50.0 points per unit in tabled values*
*| Relative Error Limit not exceeded for r .gt. 2.80*
*|---------------------------------------------------*
*
*
* NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
-4453.3*
* Etot = -148181.3735 EKtot = 0.0000 EPtot =
-148181.3735*
* BOND = 193.2917 ANGLE = 1516.4845 DIHED =
5083.5499*
* 1-4 NB = 2024.1678 1-4 EEL = 2370.5920 VDWAALS =
13450.3264*
* EELEC = -172819.7858 EHBOND = 0.0000 RESTRAINT =
0.0000*
* EKCMT = 0.0000 VIRIAL = 42217.2697 VOLUME =
439069.1196*
* SURFTEN =
0.0000*
* Density =
1.0017*
*
------------------------------------------------------------------------------
*
thank you very much
best
Albert
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Received on Fri Jul 13 2012 - 13:30:02 PDT
