Even though I have mentioned netfrc=1 in my input script, the output script
still shows it to be equal to 0, and the "skinnb" value is not being shown
in the Ewald parameter section of output file. What might be the possible
reasons?
#### input.in #####
CAP: initial minimization whole system
&cntrl
imin=1, ! choose a minimization run
maxcyc=2, ! maximum minimization cycles
ncyc=1, ! the steepest descent algorithm for the first 0-ncyc cycles,
then switches the conjugate gradient algorithm for ncyc-maxcyc cycles
cut=30.0, ! nonbonded cutoff distance in angstroms
ntb=1, ! periodic boundaries for constant volume
ntr=0, ! no position restraints
ntx=1, ! read coordinates but not velocities from ascii formatted
inpcrd coordinate file
ntpr=1, ! print to the amber mdout output file every ntpr cycles
/
&ewald
netfrc=1,skinnb=2.0d0,
/
### output.output ####
-------------------------------------------------------
Amber 18 SANDER 2018
-------------------------------------------------------
| Run on 04/15/2019 at 23:21:23
| Executable path: /home/laferrari/Downloads/amber18/bin/sander
| Working directory: /home/laferrari/Research
work/cns_honors_3_2/apo_cap/namd_amber/rst7/temp_apo_cap_namd
| Hostname: Unknown
[-O]verwriting output
File Assignments:
| MDIN: min_02.in
| MDOUT: apo_cap3.out
|INPCRD: apo_cap.rst7
| PARM: apo_cap.prmtop
|RESTRT: apo_cap3.ncrst
| REFC: refc
| MDVEL: mdvel
| MDFRC: mdfrc
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
| MTMD: mtmd
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: inptraj
Here is the input file:
CAP: initial minimization whole system
&cntrl
imin=1, ! choose a minimization run
maxcyc=2, ! maximum minimization cycles
ncyc=1, ! the steepest descent algorithm for the first 0-ncyc cycles,
then switches the conjugate gradient algorithm for ncyc-maxcyc cycles
cut=30.0, ! nonbonded cutoff distance in angstroms
ntb=1, ! periodic boundaries for constant volume
ntr=0, ! no position restraints
ntx=1, ! read coordinates but not velocities from ascii formatted
inpcrd coordinate file
ntpr=1, ! print to the amber mdout output file every ntpr cycles
/
&ewald
netfrc=1,skinnb=2.0d0,
/
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read
| peek_ewald_inpcrd: Box info found
| Setting netfrc to 0 for minimization
|Largest sphere to fit in unit cell has radius = 32.515
| New format PARM file being parsed.
| Version = 1.000 Date = 03/20/19 Time = 10:57:50
NATOM = 41598 NTYPES = 17 NBONH = 38294 MBONA = 3352
NTHETH = 7722 MTHETA = 4518 NPHIH = 15410 MPHIA = 14446
NHPARM = 0 NPARM = 0 NNB = 83502 NRES = 12056
NBONA = 3352 NTHETA = 4518 NPHIA = 14446 NUMBND = 67
NUMANG = 152 NPTRA = 191 NATYP = 36 NPHB = 1
IFBOX = 1 NMXRS = 25 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 3326531
| Hollerith 136852
| Integer 2401086
| Max Pairs 454361088
| nblistReal 499176
| nblist Int 1035587
| Total 1818695 kbytes
| Note: 1-4 EEL scale factors are being read from the topology file.
| Note: 1-4 VDW scale factors are being read from the topology file.
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
default_name
General flags:
imin = 1, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 2, ntpr = 1, ntrx = 1, ntwr =
1
iwrap = 0, ntwx = 0, ntwv = 0, ntwe =
0
ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat=
0
Potential function:
ntf = 1, ntb = 1, igb = 0, nsnb =
25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 30.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Energy minimization:
maxcyc = 2, ncyc = 1, ntmin = 1
dx0 = 0.01000, drms = 0.00010
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme =
1
vdwmeth = 1, eedmeth = 1, netfrc = 0
Box X = 100.667 Box Y = 80.729 Box Z = 65.030
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 100 NFFT2 = 80 NFFT3 = 72
Cutoff= 30.000 Tol =0.100E-04
Ewald Coefficient = 0.08521
Interpolation order = 4
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
default_name
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 11634
Sum of charges from parm topology file = -0.00000027
Forcing neutrality...
--------------------------------------------------------------------------------
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 = 0.7285E-11 at 2.543240
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 225312253
| TOTAL SIZE OF NONBOND LIST = 225312253
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -9.2916E+04 9.4080E+01 1.6147E+04 HD13 2987
BOND = 321.4453 ANGLE = 1117.2120 DIHED =
5411.5371
VDWAALS = 19766.2041 EEL = -140152.5568 HBOND =
0.0000
1-4 VDW = 2589.8056 1-4 EEL = 18030.1890 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
2 -9.3292E+04 8.3527E+01 1.4077E+04 HD13 2987
BOND = 321.2696 ANGLE = 1117.0211 DIHED =
5411.5134
VDWAALS = 19396.2240 EEL = -140157.9063 HBOND =
0.0000
1-4 VDW = 2589.7932 1-4 EEL = 18030.1318 RESTRAINT =
0.0000
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
2 -9.3292E+04 8.3527E+01 1.4077E+04 HD13 2987
BOND = 321.2696 ANGLE = 1117.0211 DIHED =
5411.5134
VDWAALS = 19396.2240 EEL = -140157.9063 HBOND =
0.0000
1-4 VDW = 2589.7932 1-4 EEL = 18030.1318 RESTRAINT =
0.0000
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| Read coords time 0.04 ( 0.13% of Total)
| Build the list 6.58 (99.80% of List )
| Other 0.01 ( 0.20% of List )
| List time 6.59 (22.87% of Nonbo)
| Short_ene time 21.99 (100.0% of Direc)
| Other 0.01 ( 0.03% of Direc)
| Direct Ewald time 22.00 (98.94% of Ewald)
| Adjust Ewald time 0.01 ( 0.03% of Ewald)
| Fill Bspline coeffs 0.01 ( 4.61% of Recip)
| Fill charge grid 0.03 (12.77% of Recip)
| Scalar sum 0.04 (19.34% of Recip)
| Grad sum 0.04 (18.37% of Recip)
| FFT time 0.10 (44.90% of Recip)
| Other 0.00 ( 0.01% of Recip)
| Recip Ewald time 0.22 ( 1.01% of Ewald)
| Other 0.00 ( 0.01% of Ewald)
| Ewald time 22.23 (77.13% of Nonbo)
| Nonbond force 28.82 (100.0% of Force)
| Bond/Angle/Dihedral 0.02 ( 0.08% of Force)
| Force time 28.85 (100.0% of Runmd)
| Runmd Time 28.85 (98.72% of Total)
| Other 0.34 ( 1.15% of Total)
| Total time 29.22 (100.0% of ALL )
| Number of list builds : 1
| Highest rstack allocated: 2345104
| Highest istack allocated: 41598
| Job began at 23:21:23.936 on 04/15/2019
| Setup done at 23:21:24.304 on 04/15/2019
| Run done at 23:21:53.158 on 04/15/2019
| wallclock() was called 126 times
|3D-RISM memory allocation summary
|Type Maximum Current
|Integer 0.00000 GB 0.00000 GB
|Real 0.00000 GB 0.00000 GB
|Logical 0.00000 GB 0.00000 GB
|Character 0.00000 GB 0.00000 GB
|---------------------------------------
|Total 0.00000 GB 0.00000 GB
On Fri, Apr 12, 2019 at 6:08 PM David A Case <david.case.rutgers.edu> wrote:
> On Fri, Apr 12, 2019, Akshay Prabhakant wrote:
>
> >I have performed single step minimization, on a solvated, counter-ionised
> >apo-CAP system, ensuring all of the parameters I could check to be the
> same
> >in amber-md and namd, but the vanderwaal and electrostatic interaction
> >energy values for both of the softwares seems to be different.
>
> Have you done everything suggested on this web page?
>
> http://ambermd.org/namd/namd_amber.html
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Apr 15 2019 - 23:30:03 PDT
