did you go from this pdb file directly to that MD step? Normally a
minimization step would be done first.
In other words, it's possible that the high energy isn't related to the
justification of the numbers.
On Fri, Sep 22, 2017 at 7:50 AM, Ana Luisa Novo de Oliveira <
analuisa.novodeoliveira.icm.uu.se> wrote:
>
> Hello!
>
>
>
> Im trying to run a system that is a octamer with more than 88000 molecules
> and my simulations crush on the 1st equilibration step, just after
> minimization.
>
>
> 1. How was wondering if the sequence to list the molecules affects the way
> that amber reads the structure, I mean, in my structure the numbers after
> 9999 are written from left to right :
>
>
> ATOM 68851 O WAT 9999 70.257 33.414 43.443 1.00 0.00
> ATOM 68852 H1 WAT 9999 69.819 32.698 42.984 1.00 0.00
> ATOM 68853 H2 WAT 9999 70.998 33.642 42.881 1.00 0.00
> TER
> ATOM 68854 O WAT 10000 67.047 28.104 49.964 1.00 0.00
> ATOM 68855 H1 WAT 10000 66.234 28.403 50.371 1.00 0.00
> ATOM 68856 H2 WAT 10000 67.543 27.709 50.682 1.00 0.00
>
>
> instead of the traditional count from right to left:
>
> ATOM 68851 O WAT 9999 70.257 33.414 43.443 1.00 0.00
> ATOM 68852 H1 WAT 9999 69.819 32.698 42.984 1.00 0.00
> ATOM 68853 H2 WAT 9999 70.998 33.642 42.881 1.00 0.00
> TER
> ATOM 68854 O WAT 10000 67.047 28.104 49.964 1.00 0.00
> ATOM 68855 H1 WAT 10000 66.234 28.403 50.371 1.00 0.00
> ATOM 68856 H2 WAT 10000 67.543 27.709 50.682 1.00 0.00
>
>
>
> 2. I don´t see any clashes but my output says:
>
>
> 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 = 0.2738E-14 at 2.422500
> | CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
> ---------------------------------------------------
> |---------------------------------------------------
> | APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
> | with 50.0 points per unit in tabled values
> | Relative Error Limit not exceeded for r .gt. 2.39
> | APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
> | with 50.0 points per unit in tabled values
> | Relative Error Limit not exceeded for r .gt. 2.84
> |---------------------------------------------------
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 144.03 PRESS =
> 0.0
> Etot = ************** EKtot = 90427.4736 EPtot =
> **************
> BOND = 2350.9848 ANGLE = 9329.9526 DIHED =
> 33698.7221
> 1-4 NB = 17712.5851 1-4 EEL = 128806.2210 VDWAALS =
> **************
> EELEC = -1078125.2640 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> Ewald error estimate: 0.7221E-03
> ------------------------------------------------------------
> ------------------
>
>
>
> Any suggestions on how to change my input file to overcome this issue?
>
>
> Input:
>
>
> # Start MD from coordinates. Assign velocities for tempi=100K and warm up
> to 150K
> # Set "restraintmask" & "restraint_wt" to the correct values for your
> system
> #
> &cntrl
> timlim=999999., imin=0,
> ntx=1,
> ntxo=1, ntpr=1000, ntwx=1000, ntwv=0, ntwe=1000, ioutfm=1,
> ntp=0, ntc=2,
> ntb=1, ntf=2, cut=9.0,
> ntt=3, temp0=150, tempi=100, ig=-1, gamma_ln=2.0,
> nstlim= 1000000, dt=0.002,
> iwrap=1, nrespa=1,
>
> /
>
> ~
>
>
>
> Thank you,
>
>
> Ana
>
>
>
> ************************************************
> Ana Oliveira, PhD
> Department of Cell and Molecular Biology
> Uppsala University
> BMC, Box 596
> SE-751 24 Uppsala
> Sweden
> email: analuisa.novodeoliveira.icm.uu.se
> Webpage: http://www.icm.uu.se/research/csb/aqvist/
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Sep 22 2017 - 05:30:02 PDT
