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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Received on Sun Jul 15 2007 - 06:07:30 PDT
