Hello,
I have been experimenting with changing force field parameters for a
model of a relatively small molecule (22 atoms). For some choices of
parameters, I see very strange results during minimization.
Specifically, the energy of successive geometries during the
minimization will sometimes jump to a higher energy than the starting
geometry. This happens with greater probability as the number of
cycles increases. I have set the non-bonded cutoff to larger than the
system, so I am unable to think of a good reason for this to happen.
I have included an mdout from one particular run. Any advice would be
appreciated.
Thank you,
Paul
-------------------------------------------------------
Amber 9 SANDER 2006
-------------------------------------------------------
| Run on 12/31/2008 at 11:25:43
[-O]verwriting output
File Assignments:
| MDIN: /scratch/347138.sugarman.rcsg.rice.edu/tmp3f954382-0ac7-46ec-8765-e863
| MDOUT: /scratch/347138.sugarman.rcsg.rice.edu/tmpb019ebfd-b323-4d91-aa65-a065
|INPCRD: /scratch/347138.sugarman.rcsg.rice.edu/tmp9f7e5acd-ae11-4e17-9e2b-a4f5
| PARM: /scratch/347138.sugarman.rcsg.rice.edu/tmpd6d09693-1319-4ae7-9f2d-99e4
|RESTRT: /scratch/347138.sugarman.rcsg.rice.edu/tmpc9b80794-c70f-4535-b93f-5778
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: /scratch/347138.sugarman.rcsg.rice.edu/tmp40e22fb1-d1de-4d06-8179-c2bc
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: inptraj
|
Here is the input file:
minimize structure
&cntrl
imin=1, igb=0, maxcyc = 50, ntb = 0, cut = 30.0, nsnb=99999999
/
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags: MPI
| NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
| *** cutoff > system size, list only builds once
|Largest sphere to fit in unit cell has radius = 30.885
| New format PARM file being parsed.
| Version = 1.000 Date = 12/31/08 Time = 11:25:43
NATOM = 22 NTYPES = 5 NBONH = 9 MBONA = 13
NTHETH = 18 MTHETA = 16 NPHIH = 30 MPHIA = 20
NHPARM = 0 NPARM = 0 NNB = 95 NRES = 1
NBONA = 13 NTHETA = 16 NPHIA = 20 NUMBND = 14
NUMANG = 21 NPTRA = 8 NATYP = 10 NPHB = 0
IFBOX = 0 NMXRS = 22 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 2696
| Hollerith 135
| Integer 21573
| Max Pairs 231
| nblistReal 264
| nblist Int 920288
| Total 3703 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
CPR
General flags:
imin = 1, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500
iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 1, ntb = 0, igb = 0, nsnb =99999999
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 30.00000, intdiel = 1.00000
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Energy minimization:
maxcyc = 50, ncyc = 10, ntmin = 1
dx0 = 0.01000, drms = 0.00010
| INFO: Old style inpcrd file read
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
CPR
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 0
| Atom division among processors:
| 0 22
Sum of charges from parm topology file = -1.00000000
| Running AMBER/MPI version on 1 nodes
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
---------------------------------------------------
eedmeth=4: Setting switch to one everywhere
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 137
| TOTAL SIZE OF NONBOND LIST = 137
NSTEP ENERGY RMS GMAX NAME NUMBER
1 7.0630E+02 2.8803E+01 1.1927E+02 C1 6
BOND = 12.8199 ANGLE = 679.2106 DIHED = 0.0001
VDWAALS = 0.0000 EEL = -5.4016 HBOND = 0.0000
1-4 VDW = 0.0000 1-4 EEL = 19.6757 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
50 8.3452E+02 7.1686E+01 2.9454E+02 HB2 3
BOND = 171.9031 ANGLE = 660.1856 DIHED = 5.2929
VDWAALS = 0.0000 EEL = -5.6018 HBOND = 0.0000
1-4 VDW = 0.0000 1-4 EEL = 2.7406 RESTRAINT = 0.0000
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
50 8.3452E+02 7.1686E+01 2.9454E+02 HB2 3
BOND = 171.9031 ANGLE = 660.1856 DIHED = 5.2929
VDWAALS = 0.0000 EEL = -5.6018 HBOND = 0.0000
1-4 VDW = 0.0000 1-4 EEL = 2.7406 RESTRAINT = 0.0000
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| Read coords time 0.00 ( 2.32% of Total)
| Fast Water setup 0.00 ( 0.12% of Total)
| Build the list 0.00 (89.72% of List )
| Other 0.00 (10.28% of List )
| List time 0.00 (17.03% of Nonbo)
| Short_ene time 0.00 (97.61% of Direc)
| Other 0.00 ( 2.39% of Direc)
| Direct Ewald time 0.00 (89.04% of Ewald)
| Force Adjust 0.00 ( 6.69% of Ewald)
| Virial junk 0.00 ( 1.37% of Ewald)
| Start sycnronization 0.00 ( 0.88% of Ewald)
| Other 0.00 ( 2.02% of Ewald)
| Ewald time 0.00 (80.91% of Nonbo)
| IPS excludes 0.00 ( 0.38% of Nonbo)
| Other 0.00 ( 1.67% of Nonbo)
| Nonbond force 0.00 (78.11% of Force)
| Bond/Angle/Dihedral 0.00 (19.62% of Force)
| FRC Collect time 0.00 ( 0.46% of Force)
| Other 0.00 ( 1.80% of Force)
| Force time 0.00 (100.0% of Runmd)
| Runmd Time 0.00 (50.92% of Total)
| Other 0.00 (46.65% of Total)
| Total time 0.01 (99.29% of ALL )
| Highest rstack allocated: 75
| Highest istack allocated: 15
| Job began at 11:25:43.038 on 12/31/2008
| Setup done at 11:25:43.041 on 12/31/2008
| Run done at 11:25:43.047 on 12/31/2008
| wallclock() was called 1260 times
-----------------------------------------------------------------------
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Received on Fri Jan 02 2009 - 01:18:40 PST
