I can't recall the details you posted at the beginning. If it is only common
elements (C,N,O,H,S) and a normal structure, it should be fine. It's
possible that if your structure is highly distorted that GB can have trouble
calculating effective radii.
If you are going to use GB, it's very important to learn about the
advantages and disadvantages of each model by reading the literature. Look
especially carefully at what models have been used successfully. Make sure
it was done recently, some older work may not have been able to take
advantage of more recent models of information. Cutoff can be important-
simulations in periodic boundary conditions can use PME to include long
range electrostatics efficiently, but in the Amber GB models no cutoff is
suggested. For large systems this can make GB much slower per energy
calculations than explicit solvent- but there might still be good reasons to
use GB (no viscosity, provides solvation free energy instead of energy).
I don't really understand your question about using igb=0 or 1. igb=0 turns
GB off, this is very different from using igb=1 or any other non-zero value.
2010/4/26 geyan <geyan.big.ac.cn>
> Hill Carlos,
> I have tried the test case and it passed,so I am sure there is nothing
> wrong with the program.
> NowI try another method,by first minimizing the whole system with IGB=0
> and after this step,I performed the minimization wiht IGB=1,now it can
> produce the normall result.
> so,why performing the minimization directly with IGB effect will make
> the system crashed?Another question is,how to make good use of the IGB,just
> simply by setting it to 0 or other values to turn it on?I have heard some
> parameters could have some effect on this model,like cutoff,I am not sure,is
> it right?if this saying is right,how to match up these parameters?
> Many thanks.
>
>
> 2010-04-26
>
>
>
> geyan
>
>
>
> 发件人： Carlos Simmerling
> 发送时间： 2010-04-25 18:56:20
> 收件人： AMBER Mailing List
> 抄送：
> 主题： Re: RE: [AMBER] about IGB
>
> did the Amber test cases pass?
> 2010/4/25 geyan <geyan.big.ac.cn>
> > Hi Ross,thank you your reply.
> > I exhibit my input and output at the end of this email. The creating
> prmtop
> > file is just following the Amber Tutorial,first load the pdb structure in
> > tleap and get the prmtop file with the saveambparm command,during the
> whole
> > step,no special happen. When I use the prmtop file adding water to run
> > sander in explicit solvent,the programm keeps working,while now in
> implicit
> > water,crashing.
> > The input and output is as follows.It maybe a little long,appreciate
> your
> > patience.
> >
> > Minimization of the entire molecular system
> > &cntrl
> > imin=1,
> > maxcyc = 5000,
> > ncyc = 250,
> > cut = 12,
> > ntb=0,
> > igb=1
> > &end
> >
> > -------------------------------------------------------
> > Amber 10 SANDER 2008
> > -------------------------------------------------------
> > | Run on 04/22/2010 at 16:27:37
> > [-O]verwriting output
> > File Assignments:
> > | MDIN: min.in
> > | MDOUT: min1.out
> > |INPCRD: com.crd
> > | PARM: com.top
> > |RESTRT: min1.rst
> > | REFC: com.crd
> > | MDVEL: mdvel
> > | MDEN: mden
> > | MDCRD: mdcrd
> > |MDINFO: mdinfo
> > |INPDIP: inpdip
> > |RSTDIP: rstdip
> > |INPTRA: inptraj
> > |
> >
> > Here is the input file:
> >
> > Minimization of the entire molecular system
> > &cntrl
> > imin=1,
> > maxcyc = 5000,
> > ncyc = 250,
> > cut = 12,
> > ntb=0,
> > igb=1
> > &end
> >
> >
> >
> --------------------------------------------------------------------------------
> > 1. RESOURCE USE:
> >
> >
> --------------------------------------------------------------------------------
> > | Flags:
> > | New format PARM file being parsed.
> > | Version = 1.000 Date = 04/09/10 Time = 22:26:16
> > NATOM = 4055 NTYPES = 17 NBONH = 1902 MBONA = 2225
> > NTHETH = 4311 MTHETA = 3102 NPHIH = 8513 MPHIA = 7264
> > NHPARM = 0 NPARM = 0 NNB = 22207 NRES = 247
> > NBONA = 2225 NTHETA = 3102 NPHIA = 7264 NUMBND = 54
> > NUMANG = 121 NPTRA = 63 NATYP = 30 NPHB = 0
> > IFBOX = 0 NMXRS = 33 IFCAP = 0 NEXTRA = 0
> > NCOPY = 0
> > Implicit solvent radii are modified Bondi radii (mbondi)
> > | Memory Use Allocated
> > | Real 260173
> > | Hollerith 24579
> > | Integer 230868
> > | Max Pairs 1
> > | nblistReal 0
> > | nblist Int 0
> > | Total 3030 kbytes
> > | Duplicated 0 dihedrals
> > | Duplicated 0 dihedrals
> >
> >
> --------------------------------------------------------------------------------
> > 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 = 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 = 0, igb = 1, nsnb =
> > 25
> > ipol = 0, gbsa = 0, iesp = 0
> > dielc = 1.00000, cut = 12.00000, intdiel = 1.00000
> > saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000
> > gbbeta = 0.00000, gbgamma = 0.00000, surften = 0.00500
> > rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.50000
> > alpb = 0
> > scnb = 2.00000, scee = 1.20000
> > Frozen or restrained atoms:
> > ibelly = 0, ntr = 0
> > Energy minimization:
> > maxcyc = 5000, ncyc = 250, ntmin = 1
> > dx0 = 0.01000, drms = 0.00010
> > | INFO: Old style inpcrd file read
> >
> >
> --------------------------------------------------------------------------------
> > 3. ATOMIC COORDINATES AND VELOCITIES
> >
> >
> --------------------------------------------------------------------------------
> >
> > begin time read from input coords = 0.000 ps
> > Number of triangulated 3-point waters found: 0
> >
> >
> --------------------------------------------------------------------------------
> > 4. RESULTS
> >
> >
> --------------------------------------------------------------------------------
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 1 NaN NaN 0.0000E+00 H5T 1
> > BOND = 156.7901 ANGLE = 1203.9996 DIHED =
> > 2628.4433
> > VDWAALS = ************* EEL = -16114.0902 EGB =
> > NaN
> > 1-4 VDW = 871.3984 1-4 EEL = 4688.0962 RESTRAINT =
> > 0.0000
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 50 NaN NaN 0.0000E+00 H5T 1
> > BOND = NaN ANGLE = NaN DIHED =
> > 12512.1894
> > VDWAALS = 0.0000 EEL = 0.0000 EGB =
> > -66813.9317
> > 1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT =
> > 0.0000
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 100 NaN NaN 0.0000E+00 H5T 1
> > BOND = NaN ANGLE = NaN DIHED =
> > 12512.1894
> > VDWAALS = 0.0000 EEL = 0.0000 EGB =
> > -66813.9317
> > 1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT =
> > 0.0000
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 150 NaN NaN 0.0000E+00 H5T 1
> > BOND = NaN ANGLE = NaN DIHED =
> > 12512.1894
> > VDWAALS = 0.0000 EEL = 0.0000 EGB =
> > -66813.9317
> > 1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT =
> > 0.0000
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 200 NaN NaN 0.0000E+00 H5T 1
> > BOND = NaN ANGLE = NaN DIHED =
> > 12512.1894
> > VDWAALS = 0.0000 EEL = 0.0000 EGB =
> > -66813.9317
> > 1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT =
> > 0.0000
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 250 NaN NaN 0.0000E+00 H5T 1
> > BOND = NaN ANGLE = NaN DIHED =
> > 12512.1894
> > VDWAALS = 0.0000 EEL = 0.0000 EGB =
> > -66813.9317
> > 1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT =
> > 0.0000
> > .... RESTARTED DUE TO LINMIN FAILURE ...
> > .... RESTARTED DUE TO LINMIN FAILURE ...
> > .... RESTARTED DUE TO LINMIN FAILURE ...
> > .... RESTARTED DUE TO LINMIN FAILURE ...
> > .... RESTARTED DUE TO LINMIN FAILURE ...
> > ***** REPEATED LINMIN FAILURE *****
> > ***** SEE http://amber.scripps.edu/Questions/linmin.html FOR MORE
> INFO
> > *****
> > FINAL RESULTS
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 271 NaN NaN 0.0000E+00 H5T 1
> > BOND = NaN ANGLE = NaN DIHED =
> > 12512.1894
> > VDWAALS = 0.0000 EEL = 0.0000 EGB =
> > -66813.9317
> > 1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT =
> > 0.0000
> >
> >
> --------------------------------------------------------------------------------
> > 5. TIMINGS
> >
> >
> --------------------------------------------------------------------------------
> > | Read coords time 0.03 ( 0.08% of Total)
> > | Calc gb radii 7.20 (23.77% of Gen B)
> > | Calc gb diag 14.01 (46.22% of Gen B)
> > | Calc gb off-diag 9.10 (30.01% of Gen B)
> > | Gen Born time 30.31 (100.0% of Nonbo)
> > | Nonbond force 30.31 (96.13% of Force)
> > | Bond/Angle/Dihedral 1.19 ( 3.79% of Force)
> > | Other 0.03 ( 0.08% of Force)
> > | Force time 31.53 (100.0% of Runmd)
> > | Runmd Time 31.53 (95.13% of Total)
> > | Other 1.58 ( 4.78% of Total)
> >
> > 2010-04-25
> >
> >
> >
> > geyan
> >
> >
> >
> > 发件人： Ross Walker
> > 发送时间： 2010-04-24 13:56:43
> > 收件人： 'AMBER Mailing List'
> > 抄送：
> > 主题： RE: [AMBER] about IGB
> >
> > Hi Geyan,
> > We'd need to see your input and output files to be able to help more. You
> > may have a bad starting structure that is being made worse when using GB.
> > How did you create your prmtop file?
> > Have you tried running the test cases to make sure everything works?
> > All the best
> > Ross
> > > -----Original Message-----
> > > From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> > > Behalf Of geyan
> > > Sent: Friday, April 23, 2010 6:09 PM
> > > To: amber-all
> > > Subject: [AMBER] about IGB
> > >
> > > Has anybody met this problem before?when performing sander by turning
> > > on the IGB flag,in my case doing minimization with IGB=1,I got the err
> > > output maily printed NaN and the rst file produced all reads NaN.As
> > > long as I turn it off,everything becames OK.Does anybody know what is
> > > wrong and how to figure it out?
> > > Due to my negligence to clean up my Inbox of my email,I release
> > > this issue again,sorry.
> > > appreciate anyone's help.
> > > --------------
> > > geyan
> > > 2010-04-24
> > >
> > >
> > >
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Received on Mon Apr 26 2010 - 04:30:04 PDT
