Thanks for your replay
I send you results
*MINIMIZATION*
-------------------------------------------------------
Amber 14 SANDER 2014
-------------------------------------------------------
| Run on 11/16/2017 at 17:04:00
| Executable path: sander.MPI
| Working directory: /home/carlos/amber14/bin
| Hostname: Unknown
[-O]verwriting output
File Assignments:
| MDIN: min.in
| MDOUT: ft-f7-base-p-MIN3.out
|INPCRD: ft-f7-base-p-MIN2.rst
| PARM: ft-f7-base-p.prmtop
|RESTRT: ft-f7-base-p-MIN3.rst
| REFC: ft-f7-base-p-MIN2.rst
| MDVEL: mdvel
| MDFRC: mdfrc
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
| MTMD: mtmd
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: inptraj
| REMLOG: rem.log
| REMTYPE: rem.type
| REMSTRIP:
| SAVEENE: saveene
|CLUSTERINF: cluster.info
| RESERVOIR: reserv/frame
| REMDDIM:
Here is the input file:
&cntrl
imin = 1,
maxcyc = 10000,
ncyc = 5000,
ntb = 1,
ntr = 0,
cut = 8
/
--------------------------------------------------------------------------------
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 = 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 = 1, igb = 0, nsnb =
25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 8.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Energy minimization:
maxcyc = 10000, ncyc = 5000, 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 = 106.253 Box Y = 100.682 Box Z = 158.003
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 108 NFFT2 = 100 NFFT3 = 160
Cutoff= 8.000 Tol =0.100E-04
Ewald Coefficient = 0.34864
Interpolation order = 4
| MPI Timing options:
| profile_mpi = 0
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
defa
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 44648
| Atom division among processors:
| 0 35871 71742 107613 143487
Sum of charges from parm topology file = -0.00000027
Forcing neutrality...
| Running AMBER/MPI version on 4 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 = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 6963387
| TOTAL SIZE OF NONBOND LIST = 27023434
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -5.9670E+05 8.0951E-02 2.1505E+01 CB 83
BOND = 47518.3706 ANGLE = 1370.2180 DIHED =
7077.0398
VDWAALS = 126133.0618 EEL = -801910.2946 HBOND =
0.0000
1-4 VDW = 1793.0096 1-4 EEL = 21317.5819 RESTRAINT =
0.0000
........................................................................................................................................
.........................................................................................................................................
NSTEP ENERGY RMS GMAX NAME NUMBER
10000 -5.9724E+05 4.8537E-02 8.1605E+00 HA 422
BOND = 47671.0351 ANGLE = 1371.5332 DIHED =
7079.0555
VDWAALS = 126938.5199 EEL = -803410.7383 HBOND =
0.0000
1-4 VDW = 1793.5357 1-4 EEL = 21317.9939 RESTRAINT =
0.0000
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
10000 -5.9724E+05 4.8537E-02 8.1605E+00 HA 422
BOND = 47671.0351 ANGLE = 1371.5332 DIHED =
7079.0555
VDWAALS = 126938.5199 EEL = -803410.7383 HBOND =
0.0000
1-4 VDW = 1793.5357 1-4 EEL = 21317.9939 RESTRAINT =
0.0000
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| Read coords time 0.44 ( 0.01% of Total)
| Build the list 2.77 ( 6.31% of List )
| Other 41.16 (93.69% of List )
| List time 43.93 ( 0.53% of Nonbo)
| Short_ene time 5778.10 (96.19% of Direc)
| Other 228.74 ( 3.81% of Direc)
| Direct Ewald time 6006.84 (72.74% of Ewald)
| Adjust Ewald time 52.60 ( 0.64% of Ewald)
| Fill Bspline coeffs 153.92 ( 7.19% of Recip)
| Fill charge grid 303.10 (14.15% of Recip)
| Scalar sum 227.27 (10.61% of Recip)
| Grad sum 424.36 (19.81% of Recip)
| FFT back comm time 399.09 (38.95% of FFT t)
| Other 625.58 (61.05% of FFT t)
| FFT time 1024.67 (47.84% of Recip)
| Other 8.34 ( 0.39% of Recip)
| Recip Ewald time 2141.67 (25.93% of Ewald)
| Force Adjust 16.46 ( 0.20% of Ewald)
| Virial junk 34.43 ( 0.42% of Ewald)
| Other 6.21 ( 0.08% of Ewald)
| Ewald time 8258.28 (99.47% of Nonbo)
| Nonbond force 8302.26 (96.57% of Force)
| Bond/Angle/Dihedral 87.78 ( 1.02% of Force)
| FRC Collect time 120.15 ( 1.40% of Force)
| Other 87.28 ( 1.02% of Force)
| Force time 8597.48 (100.0% of Runmd)
| Runmd Time 8597.48 (98.93% of Total)
| Other 92.59 ( 1.07% of Total)
| Total time 8690.52 (100.0% of ALL )
| Highest rstack allocated: 2531174
| Highest istack allocated: 51416
| Job began at 17:04:00.101 on 11/16/2017
| Setup done at 17:04:03.226 on 11/16/2017
| Run done at 19:28:50.619 on 11/16/2017
| wallclock() was called 440062 times
*HEAT RESULTS*
-------------------------------------------------------
Amber 14 SANDER 2014
-------------------------------------------------------
| Run on 11/17/2017 at 09:23:49
| Executable path: sander.MPI
| Working directory: /home/carlos/amber14/bin
| Hostname: Unknown
[-O]verwriting output
File Assignments:
| MDIN: tut3_heat.in
| MDOUT: ft-f7-base-p-HEAT.out
|INPCRD: ft-f7-base-p-MIN3.rst
| PARM: ft-f7-base-p.prmtop
|RESTRT: ft-f7-base-p-HEAT.rst
| REFC: ft-f7-base-p-MIN3.rst
| MDVEL: mdvel
| MDFRC: mdfrc
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
| MTMD: mtmd
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: inptraj
| REMLOG: rem.log
| REMTYPE: rem.type
| REMSTRIP:
| SAVEENE: saveene
|CLUSTERINF: cluster.info
| RESERVOIR: reserv/frame
| REMDDIM:
Here is the input file:
heat ras-raf
&cntrl
imin=0,irest=0,ntx=1,
nstlim=25000,dt=0.002,
ntc=2,ntf=2,
cut=8.0, ntb=1,
ntpr=500, ntwx=500,
ntt=3, gamma_ln=2.0,
tempi=0.0, temp0=300.0, ig=-1,
ntr=1, restraintmask=':1-602',
restraint_wt=2.0,
nmropt=1
/
&wt TYPE='TEMP0', istep1=0, istep2=25000,
value1=0.1, value2=300.0, /
&wt TYPE='END' /
--------------------------------------------------------------------------------
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 = 50.341
| New format PARM file being parsed.
| Version = 1.000 Date = 11/15/17 Time = 23:55:17
NATOM = 143487 NTYPES = 18 NBONH = 138631 MBONA = 4851
NTHETH = 10499 MTHETA = 6577 NPHIH = 22291 MPHIA = 20369
NHPARM = 0 NPARM = 0 NNB = 230531 NRES = 45346
NBONA = 4851 NTHETA = 6577 NPHIA = 20369 NUMBND = 67
NUMANG = 161 NPTRA = 193 NATYP = 35 NPHB = 1
IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 10563941
| Hollerith 475809
| Integer 5320403
| Max Pairs 11957250
| nblistReal 1721844
| nblist Int 6296981
| Total 189929 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
Note: ig = -1. Setting random seed to 302070 based on wallclock time in
microseconds
and disabling the synchronization of random numbers between tasks
to improve performance.
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
default_name
General flags:
imin = 0, nmropt = 1
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 500, ntrx = 1, ntwr =
500
iwrap = 0, ntwx = 500, ntwv = 0, ntwe =
0
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat=
0
Potential function:
ntf = 2, ntb = 1, igb = 0, nsnb =
25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 8.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 1
restraint_wt = 2.00000
Molecular dynamics:
nstlim = 25000, nscm = 0, nrespa = 1
t = 0.00000, dt = 0.00200, vlimit = 20.00000
Langevin dynamics temperature regulation:
ig = 302070
temp0 = 300.00000, tempi = 0.00000, gamma_ln= 2.00000
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001
NMR refinement options:
iscale = 0, noeskp = 1, ipnlty = 1, mxsub =
1
scalm = 100.00000, pencut = 0.10000, tausw = 0.10000
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme =
1
vdwmeth = 1, eedmeth = 1, netfrc = 1
Box X = 106.253 Box Y = 100.682 Box Z = 158.003
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 108 NFFT2 = 100 NFFT3 = 160
Cutoff= 8.000 Tol =0.100E-04
Ewald Coefficient = 0.34864
Interpolation order = 4
| MPI Timing options:
| profile_mpi = 0
LOADING THE CONSTRAINED ATOMS AS GROUPS
5. REFERENCE ATOM COORDINATES
defa
Mask :1-602; matches 9447 atoms
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
defa
begin time read from input coords = 0.000 ps
Begin reading energy term weight changes/NMR restraints
WEIGHT CHANGES:
TEMP0 0 25000 0.100000 300.000000 0 0
RESTRAINTS:
** No restraint defined **
Done reading weight changes/NMR restraints
Number of triangulated 3-point waters found: 44648
| Atom division among processors:
| 0 35871 71742 107613 143487
Sum of charges from parm topology file = -0.00000027
Forcing neutrality...
| Running AMBER/MPI version on 4 nodes
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
| # of SOLUTE degrees of freedom (RNDFP): 291830.
| # of SOLVENT degrees of freedom (RNDFS): 0.
| NDFMIN = 291830. NUM_NOSHAKE = 0 CORRECTED RNDFP = 291830.
| TOTAL # of degrees of freedom (RNDF) = 291830.
---------------------------------------------------
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 = 0.8332E-11 at 2.782960
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 6981466
| TOTAL SIZE OF NONBOND LIST = 27087294
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
0.0
Etot = -644586.9356 EKtot = 0.0000 EPtot =
-644586.9356
BOND = 323.1648 ANGLE = 1371.5332 DIHED =
7079.0555
1-4 NB = 1793.5357 1-4 EEL = 21317.9939 VDWAALS =
126938.5199
EELEC = -803410.7386 EHBOND = 0.0000 RESTRAINT =
0.0000
Ewald error estimate: 0.1709E-03
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 1 111 221 222
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
This is the last line, In fact I took heat.in file from tutorial 3 from
AMBER page.
Thanks a lot
2017-11-20 2:27 GMT-06:00 Bill Ross <ross.cgl.ucsf.edu>:
> Are you sure you are using the results of the minimizations as your
> starting coords?
>
> What were initial/final energies of the minimizations? (paste, please)
>
> What is your mdin file?
>
> Bill
>
>
> On 11/19/17 11:16 PM, Carlos Romero wrote:
> > Hi dear AMBER users:
> >
> > I try to make a MD for a complex (602 residues), but when I heat it, it
> > does not work, appears the following:
> > Note: This is usually a symptom of some deeper
> > problem with the energetics of the system.
> > I understand that it is because of some atoms are overlapping,
> > I analyzed coordinates from crystallographic structure and I found many
> > overlapped coordinates, but they do not disappear with minimization.
> > I started with the following min.in
> > &cntrl
> > imin = 1,
> > maxcyc = 2500,
> > ncyc = 1000,
> > ntb = 1,
> > ntr = 0,
> > cut = 8
> >
> > /
> > I did three consecutive minimizations and problem persist.
> > I would appreciate any suggestion.
> >
> > Thanks in advance.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Nov 20 2017 - 08:30:02 PST
