On Sat, Feb 21, 2015 at 6:51 AM, Fatemeh Sadat Alavi <f_alavi.sbu.ac.ir>
wrote:
>
> 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!
>
How did you conclude that you didn't have any overlaps? If your box
dimensions are "bad", then it may not be readily apparent that such
conflicts exist. I find it's usually best to use cpptraj and the
"checkoverlaps" command to check if any two atoms have periodic images that
closely overlap. So use a cpptraj script like this:
parm
complex_solvated.prmtop
trajin min2.rst
checkoverlaps *
And then run it with the command (assuming you called the script 'cpptraj.in
'):
cpptraj -i cpptraj.in
> 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?
>
What does "important difference" mean? What you should look for are large
gradients -- so look at the end of the minimization file and see what the
maximum gradient is at the end of the minimization. If your box is too
small, no amount of minimization will eliminate all bad contacts...
Also, when debugging, the most useful calculations are the ones where you
set ntpr=1 and ntwx=1 so you can actually visualize what is happening at
every step. While you said you did that, you showed *us* the files run
with ntpr=100 and just loosely described the more important files.
Actually showing us the output file that is helpful for debugging would be
better.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sat Feb 21 2015 - 13:00:02 PST
