you haven't given very much information on what you did, but the first
thing to try is run using only a single core (not in parallel) if you have
not done that already.
On Mon, Apr 2, 2018 at 4:47 AM, wangjy.dicp.ac.cn <wangjy.dicp.ac.cn> wrote:
> Hi,
> I am trying to run simulations to relax a docked system consisting a
> drug-like ligand and single-chain peptide.
> I run the mininization process successfully and get a rather normal
> structure for the following heating process.
> But odd thing happend when I started the simulation as output files
> contained no results.
> The bottom of output file is like this:
> ''
> ------------------------------------------------------------
> --------------------
> 4. RESULTS
> ------------------------------------------------------------
> --------------------
>
> | # of SOLUTE degrees of freedom (RNDFP): 109509.
> | # of SOLVENT degrees of freedom (RNDFS): 0.
> | NDFMIN = 109509. NUM_NOSHAKE = 0 CORRECTED RNDFP = 109509.
> | TOTAL # of degrees of freedom (RNDF) = 109509.
> ---------------------------------------------------
> 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
> ---------------------------------------------------
> | Local SIZE OF NONBOND LIST = 1274522
> | TOTAL SIZE OF NONBOND LIST = 16849795
> ''
> Which missing the supposed to be printed results about equilibration.
> Simulation space is suffience for this run.
> My input file is :
> ''
> Initial equibilization with protein fixed
> &cntrl
> imin = 0,
> irest = 0,
> ntx = 1,
> ntb = 1,
> cut = 10,
> ntr = 1,
> ntc = 2,
> ntf = 2,
> tempi = 0.0,
> temp0 = 300.0,
> ntt = 3,
> ig = -1,
> gamma_ln = 1.0,
> nstlim = 100000,
> dt = 0.002,
> ntpr = 1000,
> ntwx = 1000,
> ntwr = 10000,
> ioutfm = 1,
> /
> Keep protein fixed with restrains
> 10.0
> RES 1 538
> END
> END
> ''
> I tried this simulation both with Amber11 ad Amber16, they got same ouput
> files as both missing the result part.
> Did I write something wrong in the input file?
> Where should I check if such things happen?
> Thank you very much
>
> Wangjy
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Received on Mon Apr 02 2018 - 06:30:06 PDT
