Note that your van der Waals energy is off the charts - this usually
indicates bad atomic overlaps. You can use the 'check' function in
cpptraj to determine if you have atomic overlaps which may help you in
deciding whether you need more minimization or not. I recommend using
the GitHub version of cpptraj (
https://github.com/Amber-MD/cpptraj)
for this purpose since I recently made 'check' orders of magnitude
faster for systems with PBC.
-Dan
On Fri, Sep 22, 2017 at 8:48 AM, Carlos Simmerling
<carlos.simmerling.gmail.com> wrote:
> if the minimization works fine then it seems unlikely that it is a problem
> with the format of the PDB file.
> what are the energies at he end of minimization, and what did you change
> between the minimization and the MD step? that's where you should look to
> see why the energies changed.
>
> On Fri, Sep 22, 2017 at 8:18 AM, Ana Luisa Novo de Oliveira <
> analuisa.novodeoliveira.icm.uu.se> wrote:
>
>> Hello!
>>
>>
>> No, that happens just after minimization!
>>
>>
>> # Minimization with Cartesian restraints on the heavy atoms of the protein
>> # Set "restraintmask" & "restraint_wt" to the correct values for your
>> system
>> &cntrl
>> imin=1, maxcyc=5000,
>> ntpr=100,
>>
>> /
>>
>> The minimization step works fine.
>>
>> 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/
>> ________________________________
>> From: Carlos Simmerling <carlos.simmerling.gmail.com>
>> Sent: Friday, September 22, 2017 2:12:44 PM
>> To: AMBER Mailing List
>> Subject: Re: [AMBER] simulations crash
>>
>> 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/
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Fri Sep 22 2017 - 07:30:02 PDT
