 | |||||||||||||||
 |
 |
 |
|
 |
|
 |
|
 |
|
 |
|
 |
|
 |
 |
AMBER Archive (2003)
Subject: Polarizable simulation2
From: Lepsa (lepsik_at_marilyn.uochb.cas.cz)
Date: Tue Apr 01 2003 - 06:25:22 CST
- Next message: yuann: "Problem of Hbond in CARNAL"
- Previous message: S.Swaminathan: "Examples for Energy Minimisation methods"
- Next in thread: David A. Case: "Re: Polarizable simulation2"
- Reply: David A. Case: "Re: Polarizable simulation2"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
Dear AMBER community,
I have run into problems when minimizing hydrogens in a polarizable FF
(ff02). After 20 steps, the polarization term blow up (output is below).
Can you please advise me where the mistake can be and what shall I do?
Thank you in advance.
All the best,
Martin Lepsik
-------
const.V, no SHAKE, belly minimization of hydrogens
&cntrl
imin = 1, maxcyc = 1000,
ncyc = 250, drms=0.1,
ntpr = 10, ntwx=250,
cut = 10.0, nsnb = 10,
ntr = 0, ibelly=1,
ipol = 1,
&end
&ewald
indmeth = 1,
&end
Move Hydrogens
FIND
* H * *
* HC * *
* H1 * *
* HA * *
* HO * *
* HS * *
* HW * *
* HP * *
* H4 * *
* H5 * *
SEARCH
RES 1 12020
END
Move inhibitor Hydrogens
FIND
* hn * *
* hc * *
* h1 * *
* ha * *
* ho * *
* hs * *
* hw * *
* hp * *
* h4 * *
* h5 * *
SEARCH
RES 1 12020
END
END
----------------------------------------------------------------------------
---- 1. RESOURCE USE: ---------------------------------------------------------------------------- ----| Flags: getting new box info from bottom of inpcrd | peek_ewald_inpcrd: Box info found | New format PARM file being parsed. | Version = 1.000 Date = 02/28/03 Time = 14:54:24 NATOM = 31962 NTYPES = 18 NBONH = 30378 MBONA = 1605 NTHETH = 3785 MTHETA = 2178 NPHIH = 6978 MPHIA = 4116 NHPARM = 0 NPARM = 0 NNB = 56273 NRES = 9783 NBONA = 1605 NTHETA = 2178 NPHIA = 4116 NUMBND = 57 NUMANG = 119 NPTRA = 46 NATYP = 42 NPHB = 1 IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0
| Memory Use Allocated Used | Real 3800000 3260956 | Hollerith 1000000 680987 | Integer 3000000 2176651
| Max Nonbonded Pairs:12000000 | Duplicated 0 dihedrals | Duplicated 0 dihedrals
BOX TYPE: RECTILINEAR
---------------------------------------------------------------------------- ---- 2. CONTROL DATA FOR THE RUN ---------------------------------------------------------------------------- ----
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 = 10, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 250, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function: ntf = 1, ntb = 1, igb = 0, nsnb = 10 ipol = 1, gbsa = 0 dielc = 1.00000, cut = 10.00000, intdiel = 1.00000 scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms: ibelly = 1, ntr = 0
Energy minimization: maxcyc = 1000, ncyc = 250, ntmin = 1 dx0 = 0.01000, dxm = 0.50000, drms = 0.10000
Polarizable options: indmeth = 1, maxiter = 20, irstdip = 0, scaldip = 1 diptau = 11.00000, dipmass = 0.33000
Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, frc_int = 0, netfrc = 1 Box X = 65.253 Box Y = 76.336 Box Z = 79.146 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 72 NFFT2 = 80 NFFT3 = 80 Cutoff= 10.000 Tol =0.100E-04 Ewald Coefficient = 0.27511 Interpolation order = 4
Warning: Although EWALD will work with belly (for equilibration), it is not strictly correct!
LOADING THE BELLY ATOMS AS GROUPS
----- READING GROUP 1; TITLE: Move Hydrogens ALL ATOMS THAT MEET 1 OF THE FOLLOWING SPECIFICATIONS WILL BE INCLUDED IN GROUP BELOW
GRAPH NAME = * SYMBOL = H TREE SYMBOL = * RESIDUE TYPE = *
GRAPH NAME = * SYMBOL = HC TREE SYMBOL = * RESIDUE TYPE = *
GRAPH NAME = * SYMBOL = H1 TREE SYMBOL = * RESIDUE TYPE = *
GRAPH NAME = * SYMBOL = HA TREE SYMBOL = * RESIDUE TYPE = *
GRAPH NAME = * SYMBOL = HO TREE SYMBOL = * RESIDUE TYPE = *
GRAPH NAME = * SYMBOL = HS TREE SYMBOL = * RESIDUE TYPE = *
GRAPH NAME = * SYMBOL = HW TREE SYMBOL = * RESIDUE TYPE = *
GRAPH NAME = * SYMBOL = HP TREE SYMBOL = * RESIDUE TYPE = *
GRAPH NAME = * SYMBOL = H4 TREE SYMBOL = * RESIDUE TYPE = *
GRAPH NAME = * SYMBOL = H5 TREE SYMBOL = * RESIDUE TYPE = *
GRP 1 RES 1 TO 9783 Number of atoms in this group = 20763 ----- READING GROUP 2; TITLE: Move inhibitor Hydrogens ALL ATOMS THAT MEET 1 OF THE FOLLOWING SPECIFICATIONS WILL BE INCLUDED IN GROUP BELOW
GRAPH NAME = * SYMBOL = hn TREE SYMBOL = * RESIDUE TYPE = *
GRAPH NAME = * SYMBOL = hc TREE SYMBOL = * RESIDUE TYPE = *
GRAPH NAME = * SYMBOL = h1 TREE SYMBOL = * RESIDUE TYPE = *
GRAPH NAME = * SYMBOL = ha TREE SYMBOL = * RESIDUE TYPE = *
GRAPH NAME = * SYMBOL = ho TREE SYMBOL = * RESIDUE TYPE = *
GRAPH NAME = * SYMBOL = hs TREE SYMBOL = * RESIDUE TYPE = *
GRAPH NAME = * SYMBOL = hw TREE SYMBOL = * RESIDUE TYPE = *
GRAPH NAME = * SYMBOL = hp TREE SYMBOL = * RESIDUE TYPE = *
GRAPH NAME = * SYMBOL = h4 TREE SYMBOL = * RESIDUE TYPE = *
GRAPH NAME = * SYMBOL = h5 TREE SYMBOL = * RESIDUE TYPE = *
GRP 2 RES 1 TO 9783 Number of atoms in this group = 49 ----- END OF GROUP READ -----
---------------------------------------------------------------------------- ---- 3. ATOMIC COORDINATES AND VELOCITIES ---------------------------------------------------------------------------- ----
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 0
Sum of charges from parm topology file = 0.00001987 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 = 0.3251E-14 at 2.581700 | CHECK d/dx switch(x): max rel err = 0.8030E-11 at 2.732560 --------------------------------------------------- | Local SIZE OF NONBOND LIST = 8378093 | TOTAL SIZE OF NONBOND LIST = 8378093
NSTEP ENERGY RMS GMAX NAME NUMBER 1 -7.4890E+05 1.4374E+01 8.9147E+02 HG13 2363
BOND = 110.8935 ANGLE = 488.4841 DIHED = 458.4901 VDWAALS = 246.8441 EEL = -714096.7052 HBOND = 0.0000 1-4 VDW = 303.6799 1-4 EEL = -4677.1823 RESTRAINT = 0.0000 EPOLAR = -31739.0017 ETHREEB = 0.0000 Dipole convergence: rms = 0.403E-03 iters = 21.00
NSTEP ENERGY RMS GMAX NAME NUMBER 10 -7.4971E+05 1.1858E+01 4.5947E+02 HD2 1121
BOND = 124.7912 ANGLE = 480.9032 DIHED = 458.0102 VDWAALS = 75.9157 EEL = -714553.3230 HBOND = 0.0000 1-4 VDW = 303.4675 1-4 EEL = -4678.5193 RESTRAINT = 0.0000 EPOLAR = -31916.3046 ETHREEB = 0.0000 Dipole convergence: rms = 0.960E-04 iters = 9.00
NSTEP ENERGY RMS GMAX NAME NUMBER 20 -7.5353E+05 8.2393E+00 9.0293E+01 H3 1571
BOND = 889.1446 ANGLE = 427.5981 DIHED = 454.3842 VDWAALS = -213.5300 EEL = -717630.9078 HBOND = 0.0000 1-4 VDW = 301.1970 1-4 EEL = -4686.9452 RESTRAINT = 0.0000 EPOLAR = -33067.2745 ETHREEB = 0.0000 Dipole convergence: rms = 0.342E-04 iters = 2.00
NSTEP ENERGY RMS GMAX NAME NUMBER 30 -5.0563E+35 1.6097E+34 3.9360E+36 H1 3593
BOND = 11083.7352 ANGLE = 312.1750 DIHED = 437.6997 VDWAALS = -455.0935 EEL = ************* HBOND = 0.0000 1-4 VDW = 287.4668 1-4 EEL = -4694.0398 RESTRAINT = 0.0000 EPOLAR = ************* ETHREEB = 0.0000 Dipole convergence: rms = 0.219E+16 iters = 21.00
NSTEP ENERGY RMS GMAX NAME NUMBER 40 NAN NAN 0.0000E+00 N 1
BOND = nan ANGLE = nan DIHED = nan VDWAALS = -463.5263 EEL = nan HBOND = 0.0000 1-4 VDW = nan 1-4 EEL = nan RESTRAINT = 0.0000 EPOLAR = nan ETHREEB = 0.0000 Dipole convergence: rms = NAN iters = 21.00 . . . . . . . FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER 271 NAN NAN 0.0000E+00 N 1
BOND = nan ANGLE = nan DIHED = nan VDWAALS = -463.5263 EEL = nan HBOND = 0.0000 1-4 VDW = nan 1-4 EEL = nan RESTRAINT = 0.0000 EPOLAR = nan ETHREEB = 0.0000 Dipole convergence: rms = NAN iters = 21.00
***** REPEATED LINMIN FAILURE *****
- Next message: yuann: "Problem of Hbond in CARNAL"
- Previous message: S.Swaminathan: "Examples for Energy Minimisation methods"
- Next in thread: David A. Case: "Re: Polarizable simulation2"
- Reply: David A. Case: "Re: Polarizable simulation2"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
|
VU Home |
VUMC Home |
People Finder |
University Calendar
webmaster- modified on January 30, 2009 |