I have tried to run the simulation using sander.MPI and pmemd using 16 and 32 nodes following the hint given by Case.
I found no difference in the output files by commands sander.MPI and pmemd using 16 nodes. Both showing same temperature, total energy, kinectic energy, potential energy and so on.
BUT there is a difference in the output files when I use 32 nodes using both commands. I noticed in the output file generated by command sander.MPI the temperature of NSTEP = 1 is 349.14K and Etot = 34557.6758 EKtot = 27485.1983 EPtot = 7072.4775.
Suprisingly, if I run by pmemd command, the temperature at NSTEP = 1 is 367.51K and Etot = 36003.2544 EKtot = 28930.7768 EPtot = 7072.4775. The temperature at NSTEP = 2 shows NaN and shows that Etot = NaN EKtot = NaN EPtot = 7172.0266.
I have put the results of output files below for your view.
#################### OUTPUT from sander.MPI run ####################
-------------------------------------------------------
Amber 10 SANDER 2008
-------------------------------------------------------
| Run on 09/30/2010 at 14:32:27
[-O]verwriting output
File Assignments:
| MDIN: MD-malto-highLyo4800A10.in
| MDOUT: malto-highLyo4800-MD00-run1000.out
|INPCRD: e1malto-highLyo4800-Cp38.rst_100000
| PARM: malto-highLyo4800.top
|RESTRT: malto-highLyo4800-MD01-run0100.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: malto-highLyo4800-MD00-run1000.traj
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: inptraj
|
Here is the input file:
Dynamic Simulation with Constant Pressure
&cntrl
imin=0,
irest=1, ntx=5,
scnb=1.0, scee=1.2,
iwrap = 1, nscm=1000,
ntt=2, temp0=348.0, tautp=1.0,
ntb = 2, ntp=1, taup=0.2,
ntf=2,ntc=2,
nstlim=10, dt=0.001,
ntwe=100, ntwx=100, ntpr=1, ntwr=-50000,
cut = 9.0
/
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags: MPI
getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read
| peek_ewald_inpcrd: Box info found
|Largest sphere to fit in unit cell has radius = 26.401
| New format PARM file being parsed.
| Version = 1.000 Date = 07/09/10 Time = 18:22:02
NATOM = 35136 NTYPES = 9 NBONH = 26176 MBONA = 9216
NTHETH = 27648 MTHETA = 12032 NPHIH = 45312 MPHIA = 21248
NHPARM = 0 NPARM = 0 NNB = 138752 NRES = 5056
NBONA = 9216 NTHETA = 12032 NPHIA = 21248 NUMBND = 9
NUMANG = 14 NPTRA = 20 NATYP = 9 NPHB = 1
IFBOX = 1 NMXRS = 81 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 1877716
| Hollerith 215874
| Integer 2211637
| Max Pairs 649528
| nblistReal 421632
| nblist Int 1567676
| Total 36107 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
General flags:
imin = 0, nmropt = 0
Nature and format of input:
ntx = 5, irest = 1, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 1, ntrx = 1, ntwr = -50000
iwrap = 1, ntwx = 100, ntwv = 0, ntwe = 100
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 2, ntb = 2, igb = 0, nsnb = 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 9.00000, intdiel = 1.00000
scnb = 1.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 10, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00100, vlimit = 20.00000
Anderson (strong collision) temperature regulation:
ig = 71277, vrand = 1000
temp0 = 348.00000, tempi = 0.00000
Pressure regulation:
ntp = 1
pres0 = 1.00000, comp = 44.60000, taup = 0.20000
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
vdwmeth = 1, eedmeth = 1, netfrc = 1
Box X = 116.539 Box Y = 52.802 Box Z = 59.727
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 120 NFFT2 = 54 NFFT3 = 60
Cutoff= 9.000 Tol =0.100E-04
Ewald Coefficient = 0.30768
Interpolation order = 4
| MPI Timing options:
| profile_mpi = 0
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 1950.000 ps
Number of triangulated 3-point waters found: 4800
| Atom division among processors:
| 0 1134 2268 3402 4536 5670 6804 7938
| 9072 10206 11340 12474 13608 14742 15876 17010
| 18144 19278 20412 21465 22518 23571 24624 25677
| 26730 27780 28830 29883 30933 31983 33036 34086
| 35136
Sum of charges from parm topology file = 0.00000000
Forcing neutrality...
| Running AMBER/MPI version on 32 nodes
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
| # of SOLUTE degrees of freedom (RNDFP): 79232.
| # of SOLVENT degrees of freedom (RNDFS): 0.
| NDFMIN = 79229. NUM_NOSHAKE = 0 CORRECTED RNDFP = 79229.
| TOTAL # of degrees of freedom (RNDF) = 79229.
---------------------------------------------------
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 = 0.3338E-14 at 2.509280
| CHECK d/dx switch(x): max rel err = 0.8261E-11 at 2.768360
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 319099
| TOTAL SIZE OF NONBOND LIST = 9514333
NSTEP = 1 TIME(PS) = 1950.001 TEMP(K) = 349.14 PRESS = -272.7
Etot = 34557.6758 EKtot = 27485.1983 EPtot = 7072.4775
BOND = 4508.4256 ANGLE = 13735.4180 DIHED = 3647.8562
1-4 NB = 5964.5867 1-4 EEL = 96761.8688 VDWAALS = -5148.2958
EELEC = -112397.3820 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 5290.0237 VIRIAL = 7454.2445 VOLUME = 367526.4612
Density = 0.9813
Ewald error estimate: 0.4246E-04
------------------------------------------------------------------------------
NSTEP = 2 TIME(PS) = 1950.002 TEMP(K) = 348.66 PRESS = -273.4
Etot = 34558.0751 EKtot = 27447.0760 EPtot = 7110.9991
BOND = 4491.8852 ANGLE = 13785.9250 DIHED = 3647.2267
1-4 NB = 5973.5736 1-4 EEL = 96751.5289 VDWAALS = -5148.1766
EELEC = -112390.9637 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 5290.1781 VIRIAL = 7459.6275 VOLUME = 367504.0266
Density = 0.9814
Ewald error estimate: 0.3314E-04
------------------------------------------------------------------------------
NSTEP = 3 TIME(PS) = 1950.003 TEMP(K) = 347.97 PRESS = -272.1
Etot = 34558.7896 EKtot = 27392.4225 EPtot = 7166.3672
BOND = 4480.8944 ANGLE = 13849.5013 DIHED = 3647.1350
1-4 NB = 5982.2156 1-4 EEL = 96743.2780 VDWAALS = -5147.9222
EELEC = -112388.7349 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 5290.2877 VIRIAL = 7449.2919 VOLUME = 367481.5381
Density = 0.9814
Ewald error estimate: 0.2756E-04
------------------------------------------------------------------------------
NSTEP = 4 TIME(PS) = 1950.004 TEMP(K) = 347.27 PRESS = -269.2
Etot = 34559.5005 EKtot = 27337.5234 EPtot = 7221.9772
BOND = 4477.2883 ANGLE = 13908.8890 DIHED = 3647.4743
1-4 NB = 5989.3177 1-4 EEL = 96737.5769 VDWAALS = -5147.1893
EELEC = -112391.3798 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 5290.2198 VIRIAL = 7425.8397 VOLUME = 367459.1574
Density = 0.9815
Ewald error estimate: 0.1461E-04
------------------------------------------------------------------------------
NSTEP = 5 TIME(PS) = 1950.005 TEMP(K) = 346.77 PRESS = -265.0
Etot = 34559.9268 EKtot = 27298.4050 EPtot = 7261.5218
BOND = 4481.6839 ANGLE = 13948.0231 DIHED = 3648.1200
1-4 NB = 5994.0007 1-4 EEL = 96734.7097 VDWAALS = -5145.8220
EELEC = -112399.1936 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 5289.8485 VIRIAL = 7391.9507 VOLUME = 367437.0182
Density = 0.9816
Ewald error estimate: 0.1593E-04
------------------------------------------------------------------------------
NSTEP = 6 TIME(PS) = 1950.006 TEMP(K) = 346.62 PRESS = -259.8
Etot = 34559.8010 EKtot = 27286.1777 EPtot = 7273.6233
BOND = 4493.2354 ANGLE = 13956.9265 DIHED = 3648.9738
1-4 NB = 5995.8066 1-4 EEL = 96734.7782 VDWAALS = -5143.6431
EELEC = -112412.4540 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 5289.0590 VIRIAL = 7349.8109 VOLUME = 367415.2252
Density = 0.9816
Ewald error estimate: 0.1181E-04
------------------------------------------------------------------------------
NSTEP = 7 TIME(PS) = 1950.007 TEMP(K) = 346.84 PRESS = -253.5
Etot = 34559.1175 EKtot = 27303.9857 EPtot = 7255.1317
BOND = 4509.6100 ANGLE = 13934.5852 DIHED = 3650.0086
1-4 NB = 5994.8040 1-4 EEL = 96737.7024 VDWAALS = -5140.6701
EELEC = -112430.9084 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 5287.7577 VIRIAL = 7298.4330 VOLUME = 367393.8593
Density = 0.9817
Ewald error estimate: 0.2961E-05
------------------------------------------------------------------------------
NSTEP = 8 TIME(PS) = 1950.008 TEMP(K) = 347.38 PRESS = -245.3
Etot = 34558.0937 EKtot = 27346.4299 EPtot = 7211.6639
BOND = 4527.2341 ANGLE = 13888.9260 DIHED = 3651.2964
1-4 NB = 5991.5594 1-4 EEL = 96743.2261 VDWAALS = -5137.0215
EELEC = -112453.5566 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 5285.8760 VIRIAL = 7231.5976 VOLUME = 367373.0106
Density = 0.9817
Ewald error estimate: 0.1790E-05
------------------------------------------------------------------------------
NSTEP = 9 TIME(PS) = 1950.009 TEMP(K) = 348.08 PRESS = -234.4
Etot = 34556.8838 EKtot = 27401.5605 EPtot = 7155.3232
BOND = 4541.8809 ANGLE = 13834.0914 DIHED = 3652.9920
1-4 NB = 5986.9417 1-4 EEL = 96750.9244 VDWAALS = -5132.2203
EELEC = -112479.2868 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 5283.3673 VIRIAL = 7142.7613 VOLUME = 367352.8327
Density = 0.9818
Ewald error estimate: 0.2417E-05
------------------------------------------------------------------------------
writing malto-highLyo4800-MD01-run0100.rst_10
NSTEP = 10 TIME(PS) = 1950.010 TEMP(K) = 348.76 PRESS = -220.1
Etot = 34555.7238 EKtot = 27454.8002 EPtot = 7100.9236
BOND = 4549.5841 ANGLE = 13786.0362 DIHED = 3655.2698
1-4 NB = 5981.8661 1-4 EEL = 96760.2179 VDWAALS = -5125.5763
EELEC = -112506.4742 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 5280.2083 VIRIAL = 7025.5151 VOLUME = 367333.5465
Density = 0.9818
Ewald error estimate: 0.2498E-05
------------------------------------------------------------------------------
A V E R A G E S O V E R 10 S T E P S
NSTEP = 10 TIME(PS) = 1950.010 TEMP(K) = 347.75 PRESS = -256.5
Etot = 34558.3588 EKtot = 27375.3579 EPtot = 7183.0008
BOND = 4506.1722 ANGLE = 13862.8322 DIHED = 3649.6353
1-4 NB = 5985.4672 1-4 EEL = 96745.5811 VDWAALS = -5141.6537
EELEC = -112425.0334 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 5287.6826 VIRIAL = 7322.9072 VOLUME = 367427.6676
Density = 0.9816
Ewald error estimate: 0.1552E-04
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 10 TIME(PS) = 1950.010 TEMP(K) = 0.86 PRESS = 17.3
Etot = 1.2783 EKtot = 67.6272 EPtot = 68.6299
BOND = 24.6264 ANGLE = 72.8782 DIHED = 2.6179
1-4 NB = 9.6021 1-4 EEL = 9.5673 VDWAALS = 7.4016
EELEC = 39.5292 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 3.3057 VIRIAL = 140.6527 VOLUME = 61.9001
Density = 0.0002
Ewald error estimate: 0.1373E-04
------------------------------------------------------------------------------
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
|>>>>>>>>PROFILE of Average TIMES>>>>>>>>>
| Read coords time 0.00 ( 0.16% of Total)
| Build the list 0.03 (36.65% of List )
| Other 0.05 (63.35% of List )
| List time 0.07 (17.01% of Nonbo)
| Short_ene time 0.16 (88.26% of Direc)
| Other 0.02 (11.74% of Direc)
| Direct Ewald time 0.18 (51.13% of Ewald)
| Adjust Ewald time 0.01 ( 1.60% of Ewald)
| Self Ewald time 0.00 ( 0.10% of Ewald)
| Fill Bspline coeffs 0.01 (10.66% of Recip)
| Fill charge grid 0.01 (12.86% of Recip)
| Scalar sum 0.00 ( 4.77% of Recip)
| Grad sum 0.01 (14.60% of Recip)
| FFT back comm time 0.03 (51.11% of FFT t)
| Other 0.03 (48.89% of FFT t)
| FFT time 0.05 (53.90% of Recip)
| Other 0.00 ( 3.21% of Recip)
| Recip Ewald time 0.10 (28.11% of Ewald)
| Force Adjust 0.02 ( 7.02% of Ewald)
| Virial junk 0.01 ( 2.59% of Ewald)
| Start sycnronization 0.00 ( 0.01% of Ewald)
| Other 0.03 ( 9.44% of Ewald)
| Ewald time 0.36 (82.98% of Nonbo)
| Other 0.00 ( 0.01% of Nonbo)
| Nonbond force 0.43 (89.07% of Force)
| Bond/Angle/Dihedral 0.01 ( 1.95% of Force)
| FRC Collect time 0.03 ( 5.27% of Force)
| Other 0.02 ( 3.71% of Force)
| Force time 0.48 (76.59% of Runmd)
| Shake time 0.02 ( 2.79% of Runmd)
| Verlet update time 0.08 (12.89% of Runmd)
| Ekcmr time 0.02 ( 3.14% of Runmd)
| CRD distribute time 0.02 ( 3.54% of Runmd)
| Other 0.01 ( 1.05% of Runmd)
| Runmd Time 0.63 (27.81% of Total)
| Other 1.63 (72.03% of Total)
| Total time 2.26 (100.0% of ALL )
| Number of list builds : 1
| Highest rstack allocated: 136646
| Highest istack allocated: 3904
| Job began at 14:32:27.607 on 09/30/2010
| Setup done at 14:32:29.236 on 09/30/2010
| Run done at 14:32:30.994 on 09/30/2010
| wallclock() was called 582 times
################### End of output by sander.MPI ####################
#################### Output from PMEMD run ###################
-------------------------------------------------------
Amber 10 SANDER 2008
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 10
| Run on 09/30/2010 at 14:40:32
[-O]verwriting output
File Assignments:
| MDIN: MD-malto-highLyo4800A10.in
| MDOUT: malto-highLyo4800-MD00-run1000.out
| INPCRD: e1malto-highLyo4800-Cp38.rst_100000
| PARM: malto-highLyo4800.top
| RESTRT: malto-highLyo4800-MD01-run0100.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: malto-highLyo4800-MD00-run1000.traj
| MDINFO: mdinfo
|LOGFILE: logfile
Here is the input file:
Dynamic Simulation with Constant Pressure
&cntrl
imin=0,
irest=1, ntx=5,
scnb=1.0, scee=1.2,
iwrap = 1, nscm=1000,
ntt=2, temp0=348.0, tautp=1.0,
ntb = 2, ntp=1, taup=0.2,
ntf=2,ntc=2,
nstlim=10, dt=0.001,
ntwe=100, ntwx=100, ntpr=1, ntwr=-50000,
cut = 9.0
/
| Conditional Compilation Defines Used:
| MPI
| SLOW_INDIRECTVEC
| PUBFFT
| MKL
| Largest sphere to fit in unit cell has radius = 26.401
| New format PARM file being parsed.
| Version = 1.000 Date = 07/09/10 Time = 18:22:02
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
getting new box info from bottom of inpcrd
NATOM = 35136 NTYPES = 9 NBONH = 26176 MBONA = 9216
NTHETH = 27648 MTHETA = 12032 NPHIH = 45312 MPHIA = 21248
NHPARM = 0 NPARM = 0 NNB = 138752 NRES = 5056
NBONA = 9216 NTHETA = 12032 NPHIA = 21248 NUMBND = 9
NUMANG = 14 NPTRA = 20 NATYP = 9 NPHB = 1
IFBOX = 1 NMXRS = 81 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Coordinate Index Table dimensions: 21 9 10
| Direct force subcell size = 5.5495 5.8669 5.9727
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
General flags:
imin = 0, nmropt = 0
Nature and format of input:
ntx = 5, irest = 1, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 1, ntrx = 1, ntwr = -50000
iwrap = 1, ntwx = 100, ntwv = 0, ntwe = 100
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 2, ntb = 2, igb = 0, nsnb = 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 9.00000, intdiel = 1.00000
scnb = 1.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 10, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00100, vlimit = 20.00000
Anderson (strong collision) temperature regulation:
ig = 71277, vrand = 1000
temp0 = 348.00000, tempi = 0.00000
Pressure regulation:
ntp = 1
pres0 = 1.00000, comp = 44.60000, taup = 0.20000
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001
| Intermolecular bonds treatment:
| no_intermolecular_bonds = 1
| Energy averages sample interval:
| ene_avg_sampling = 1
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
vdwmeth = 1, eedmeth = 1, netfrc = 1
Box X = 116.539 Box Y = 52.802 Box Z = 59.727
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 120 NFFT2 = 54 NFFT3 = 60
Cutoff= 9.000 Tol =0.100E-04
Ewald Coefficient = 0.30768
Interpolation order = 4
| PMEMD ewald parallel performance parameters:
| block_fft = 1
| fft_blk_y_divisor = 4
| excl_recip = 0
| excl_master = 0
| atm_redist_freq = 320
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 1950.000 ps
Number of triangulated 3-point waters found: 4800
Sum of charges from parm topology file = 0.00000000
Forcing neutrality...
| Dynamic Memory, Types Used:
| Reals 1322536
| Integers 2252183
| Nonbonded Pairs Initial Allocation: 662038
| Running AMBER/MPI version on 32 nodes
--------------------------------------------------------------------------------
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 = 0.3338E-14 at 2.509280
| CHECK d/dx switch(x): max rel err = 0.8261E-11 at 2.768360
---------------------------------------------------
NSTEP = 1 TIME(PS) = 1950.001 TEMP(K) = 367.51 PRESS = -94.0
Etot = 36003.2544 EKtot = 28930.7768 EPtot = 7072.4775
BOND = 4508.4256 ANGLE = 13735.4180 DIHED = 3647.8562
1-4 NB = 5964.5867 1-4 EEL = 96761.8688 VDWAALS = -5148.2958
EELEC = -112397.3820 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 5290.0237 VIRIAL = 6035.5941 VOLUME = 367526.4612
Density = 0.9813
Ewald error estimate: 0.4246E-04
------------------------------------------------------------------------------
vlimit exceeded for step 1; vmax = 22.3237
NSTEP = 2 TIME(PS) = 1950.002 TEMP(K) = NaN PRESS = -6625.7
Etot = NaN EKtot = NaN EPtot = 7172.0266
BOND = 4493.8546 ANGLE = 13808.2993 DIHED = 3647.7975
1-4 NB = 5974.1058 1-4 EEL = 96751.6369 VDWAALS = -5149.8915
EELEC = -112353.7758 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 6183.7853 VIRIAL = 58759.5962 VOLUME = 367518.6788
Density = 0.9813
Ewald error estimate: 0.3771E-04
------------------------------------------------------------------------------
Coordinate resetting (shake) was not accomplished
within 3000 iterations
#################### End of PMEMD output file ####################
Could you kindly give some suggestion how to overcome this issue?
Thank you.
Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
Malaysia
vjramana.gmail.com
--- On Wed, 29/9/10, case <case.biomaps.rutgers.edu> wrote:
> From: case <case.biomaps.rutgers.edu>
> Subject: Re: [AMBER] running pmemd fails
> To: "AMBER Mailing List" <amber.ambermd.org>
> Date: Wednesday, 29 September, 2010, 19:39
> On Wed, Sep 29, 2010, Vijay Manickam
> Achari wrote:
>
> > According to Case's advice, I have tried to run small
> number of steps
> > using fewer nodes. It runs in 16 nodes but more than
> this number it
> > terminates indicating the same problem about as
> shake.
> >
> > Why this happens and where the mistake could be?
>
> Did you run a 10-step simulation and look at the
> output on every step? Are
> there differences at step 1? You need to look as
> closely as you can at pmemd
> below and above 16 nodes, and versus sander. Saying
> there is a shake error is
> of no new help--it just means something is wrong.
> Finding the exact
> differences in short outputs may help in locating the
> problem. I don't recall
> hearing of a symptom like this before, so additional (and
> detailed)
> information is likely to be required.
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Sep 29 2010 - 23:30:03 PDT
