Hi
I am running minimization in 2 steps:
1; Holding the solute fixed
2; Minimizing the entire system
and the moving to run heating with following input:
20ps MD with res on protein
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 1,
cut = 10.0,
ntr = 1,
ntc = 2,
ntf = 2,
tempi = 0.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 10000, dt = 0.002
ntpr = 100, ntwx = 100, ntwr = 1000
/
Keep protein fixed with weak restraints
10.0
RES 1 300
END
END
still the run persists with same vlimit exceeded error , output is;
-------------------------------------------------------
Amber 12 SANDER 2012
-------------------------------------------------------
| Run on 02/21/2015 at 13:07:22
File Assignments:
| MDIN: heat1.in
| MDOUT: heat1.out
|INPCRD: min2.rst
| PARM: complex_solvated.prmtop
|RESTRT: heat1.rst
| REFC: min2.rst
| MDVEL: mdvel
| MDEN: mden
| MDCRD: heat1.mdcrd
|MDINFO: mdinfo
| MTMD: mtmd
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: inptraj
|
Here is the input file:
20ps MD with res on protein
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 1,
cut = 10.0,
ntr = 1,
ntc = 2,
ntf = 2,
tempi = 0.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 10000, dt = 0.002
ntpr = 100, ntwx = 100, ntwr = 1000
/
Keep protein fixed with weak restraints
10.0
RES 1 300
END
END
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
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 = 37.155
| New format PARM file being parsed.
| Version = 1.000 Date = 02/16/15 Time = 16:53:11
NATOM = 41556 NTYPES = 17 NBONH = 39762 MBONA = 1833
NTHETH = 4028 MTHETA = 2484 NPHIH = 8017 MPHIA = 6084
NHPARM = 0 NPARM = 0 NNB = 70329 NRES = 12884
NBONA = 1833 NTHETA = 2484 NPHIA = 6084 NUMBND = 48
NUMANG = 103 NPTRA = 50 NATYP = 32 NPHB = 1
IFBOX = 1 NMXRS = 73 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 2328524
| Hollerith 137554
| Integer 1654204
| Max Pairs 23936256
| nblistReal 498672
| nblist Int 1629857
| Total 128954 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 = 0, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 100, ntrx = 1, ntwr =
1000
iwrap = 0, ntwx = 100, 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 = 10.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 1
restraint_wt = 0.00000
Molecular dynamics:
nstlim = 10000, nscm = 0, nrespa = 1
t = 0.00000, dt = 0.00200, vlimit = 20.00000
Langevin dynamics temperature regulation:
ig = 71277
temp0 = 300.00000, tempi = 0.00000, gamma_ln= 1.00000
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 = 77.725 Box Y = 74.310 Box Z = 87.672
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 80 NFFT2 = 75 NFFT3 = 90
Cutoff= 10.000 Tol =0.100E-04
Ewald Coefficient = 0.27511
Interpolation order = 4
LOADING THE CONSTRAINED ATOMS AS GROUPS
5. REFERENCE ATOM COORDINATES
defa
----- READING GROUP 1; TITLE:
Keep protein fixed with weak restraints
GROUP 1 HAS HARMONIC CONSTRAINTS 10.00000
GRP 1 RES 1 TO 300
Number of atoms in this group = 3804
----- END OF GROUP READ -----
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
defa
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 12664
Sum of charges from parm topology file = -0.00000010
Forcing neutrality...
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
| # of SOLUTE degrees of freedom (RNDFP): 84906.
| # of SOLVENT degrees of freedom (RNDFS): 0.
| NDFMIN = 84906. NUM_NOSHAKE = 0 CORRECTED RNDFP = 84906.
| TOTAL # of degrees of freedom (RNDF) = 84906.
---------------------------------------------------
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 = 0.3145E-14 at 2.553520
| CHECK d/dx switch(x): max rel err = 0.7937E-11 at 2.748560
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 12818359
| TOTAL SIZE OF NONBOND LIST = 12818359
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
0.0
Etot = -180132.7391 EKtot = 0.0000 EPtot =
-180132.7391
BOND = 124.8281 ANGLE = 582.1677 DIHED =
2268.6713
1-4 NB = 727.9131 1-4 EEL = 7589.8215 VDWAALS =
33078.4512
EELEC = -224504.5920 EHBOND = 0.0000 RESTRAINT =
0.0000
Ewald error estimate: 0.1060E-03
------------------------------------------------------------------------------
vlimit exceeded for step 1; vmax = 71.5441
....
after that, I run a short simulation with ntpr=1 ntwx=1 nstlim=100 ,
visualize my trajectory with Chimera, but I didn't have overlap in my system
and My ligand ( non_standard residue) allocated in right place!
but I have important difference between energy at step 0 of the dynamics and
last step of minimization!!!How should I look into the matter?
Thank you
Best regards.
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Received on Sat Feb 21 2015 - 04:00:02 PST
