how can i change the dimensions of the water box. What do you mean by
"half again as big"?
here's my leap file if it's helpful:
source /home//Glycam04/1004leaprc.Glycam_04
loadamberparams /usr/local/amber9/dat/leap/parm/frcmod.tip4p
loadamberparams /home/Glycam04/Glycam_04l.dat
loadamberprep beta.prep
x = sequence {OME 0AU}
savepdb x beta_ome.pdb
saveamberprep x beta_ome.prep
saveamberparm x beta_ome.top beta_ome.crd
solvateBox x TIP4PBOX 7
savepdb x beta_ome_sol.pdb
saveamberparm x beta_ome_sol.top beta_ome_sol.crd
check x
On 7/12/07, Robert Duke <rduke.email.unc.edu> wrote:
> You have something like an 18 angstrom x 20 angstrom x 20 angstrom box. The
> box has to be big enough to hold a circumscribed sphere with radius cut +
> skinnb. I don't see you using constant pressure, so I am not sure that the
> box sizes would have readjusted, but in the error output the box has an x
> dimension of very slightly less than 18 angstrom, so if cut + skinnb is 9,
> the box is too small. Folks, at least in my opinion, it is not a good idea
> to mess around with a box this small. Make the dimensions at least half
> again as big. Yes, the very small system runs faster, but if there is any
> density correction under NPT, then your efforts are wasted. And going to
> shorter cutoffs than 8 is probably not a great idea. You CAN reduce the
> skinnb value a bit, but that is a pretty inefficient thing to do too as
> pairlist building, which is expensive, will occur significantly more
> frequently. I presume that the reason folks hit this with TIP4P is mostly
> because we have some test case boxes out there for TIP4P that are really
> small. They are intended for short tests, not production.
> Best Regards - Bob Duke
>
> ----- Original Message -----
> From: "Hashem Taha" <hashemt.gmail.com>
> To: <amber.scripps.edu>
> Sent: Thursday, July 12, 2007 4:31 PM
> Subject: AMBER: Molecular Dynamic Simulations using TIP4P water - Please
> Help
>
>
> > Hi,
> >
> > this is my problem. I am trying to do MD simulations using TIP4P
> > water. I have done them using TIP3P and they worked fine. My input
> > files are below. I first do a minimization of the water molecules,
> > then minimization of the entire system (water+sugar). then i do
> > annealling. Up to this point, everything is ok. But when i try to do a
> > short MD i get the following errors:
> >
> > THESE ARE THE INPUT FILES USED:
> > ---for minimizing water-----
> >
> > Constant Volume Minimization
> > # Control section
> > &cntrl
> > ntwx = 50, ntpr = 1, ntwr = 1,
> > scnb = 1.0, scee = 1.0, nsnb = 25, dielc = 1, cut = 8.0,
> > ntb = 1,
> > maxcyc = 2000, ntmin = 0, dx0 = 0.01, dxm = 0.5, drms = 0.0001,
> > ntp = 0,
> > ibelly = 0, ntr = 1,
> > imin = 1,
> > &end
> > Group Input for restrained atoms
> > 5.0
> > RES 1 2
> > END
> > END
> >
> > ---for minimizing entire system----
> >
> > Constant Volume Minimization
> > # Control section
> > &cntrl
> > ntwx = 50, ntpr = 1, ntwr = 1,
> > scnb = 1.0, scee = 1.0, nsnb = 25, dielc = 1, cut = 8.0,
> > ntb = 1,
> > maxcyc = 2000, ncyc = 100, dx0 = 0.01, dxm = 0.5, drms = 0.0001,
> > ntp = 0,
> > ibelly = 0, ntr = 0,
> > imin = 1, ntmin = 1,
> > &end
> >
> > ---annealling-----
> >
> > Dynamic Simulation with Constant Volume
> >
> > # Control section
> > &cntrl
> > ntwx = 100, ntpr = 50, ntwr = 1,
> > ntt = 1, temp0 = 300.0, tempi = 5.0, tautp = 1.0,
> > scnb = 1.0, scee = 1.0, dielc = 1, cut = 6.0,
> > ntb = 2, ntc = 2, ntf = 2,
> > nstlim = 50000, dt = 0.0020,
> > ntp = 1, taup = 0.1, comp = 44.6, pres0 = 1.0,
> > ibelly = 0, ntr = 0,
> > imin = 0, irest = 0, ntx = 1, nmropt = 1,
> > &end
> >
> > &ewald
> > skinnb = 2.0,
> > nbflag = 1,
> > &end
> >
> > &wt
> > type = 'TEMP0', istep1 = 1, istep2 = 25000, value1 = 5.0, value2 = 300.0,
> > &end
> >
> > &wt
> > type = 'TEMP0', istep1 = 25001, istep2 = 50000, value1 = 300.0, value2 =
> > 5.0,
> > &end
> >
> > &wt
> > type='END'
> > &end
> > &rst IAT(1) = 0 &end
> > END
> >
> > ---short MD---
> > Dynamic Simulation with Constant Volume
> >
> > # Control section
> > &cntrl
> > ntwx = 100, ntpr = 100, ntwr = 1,
> > ntt = 1, temp0 = 300.0, tempi = 5.0, tautp = 1.0,
> > scnb = 1.0, scee = 1.0, dielc = 1, cut = 8.0,
> > ntb = 2, ntc = 2, ntf = 2,
> > nstlim = 75000, dt = 0.0020,
> > ntp = 1, taup = 0.1, comp = 44.6, pres0 = 1.0,
> > ibelly = 0, ntr = 0,
> > imin = 0, irest = 0, ntx = 1, nmropt = 1,
> > &end
> >
> > &ewald
> > skinnb = 1.0,
> > nbflag = 1,
> > &end
> >
> > &wt
> > type = 'TEMP0', istep1 = 1, istep2 = 75000, value1 = 5.0, value2 = 300.0,
> > &end
> >
> > &wt
> > type = 'TEMP0', istep1 = 35001, istep2 = 75000, value1 = 300.0,
> > value2 = 300.0,
> > &end
> >
> > &wt
> > type='END'
> > &end
> > &rst IAT(1) = 0 &end
> > END
> >
> > THESE ARE THE ERRORS AT THE END OF SHORTMD.OUT:
> >
> > Ewald parameters:
> > verbose = 0, ew_type = 0, nbflag = 1, use_pme =
> > 1
> > vdwmeth = 1, eedmeth = 1, netfrc = 1
> > Box X = 17.998 Box Y = 20.229 Box Z = 20.215
> > Alpha = 90.000 Beta = 90.000 Gamma = 90.000
> > NFFT1 = 18 NFFT2 = 20 NFFT3 = 20
> > Cutoff= 8.000 Tol =0.100E-04
> > Ewald Coefficient = 0.34864
> > Interpolation order = 4
> >
> > Ewald PARAMETER RANGE CHECKING:
> > parameter skinnb+cutoffnb: (nonbond list cut) has value 0.90000E+01
> > This is outside the legal range
> > Lower limit: 0.00000E+00 Upper limit: 0.89989E+01
> > Check ew_legal.h
> >
> > I tried changing the cut value from 8 to 7.5, but this was
> > unsuccessful for the production dynamics as you may have seen in my
> > previous message.
> >
> > Can you let me know what i am doing wrong. Also, please let me know if
> > you need anymore information.
> > -----------------------------------------------------------------------
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> >
>
>
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Received on Sun Jul 15 2007 - 06:07:30 PDT
