Hi Nick,
You haven't given it enough time to heat up. You have gamma_ln=0.01 which is very low and then the run is just for 10ps so it's too short for the langevin thermostat (which is very weak with that gamma_ln setting) to raise the temperature. I'd suggest setting gamma_ln=1.0 or maybe even 5.0 for the heating stage and give it around 20ps or so minimum time wise.
All the best
Ross
> On Nov 1, 2016, at 10:34, Nikolay N. Kuzmich <nnkuzmich.gmail.com> wrote:
>
> Dear Amber users,
>
> when I ran the 1st stage of heating simulation from 0 to 100K,
>
> the ultimate temperature didn't surpass 12K.
> Here are the last steps from output file:
>
> NSTEP = 19950 TIME(PS) = 9.975 TEMP(K) = 11.36 PRESS =
> 0.0
> Etot = -8576.1998 EKtot = 92.4017 EPtot =
> -8668.6016
> BOND = 134.2874 ANGLE = 457.9412 DIHED =
> 2215.2082
> 1-4 NB = 655.3423 1-4 EEL = 7913.8875 VDWAALS =
> -1791.1388
> EELEC = -14827.7755 EGB = -3426.3539 RESTRAINT =
> 0.0000
> ------------------------------------------------------------------------------
>
> | RE_POSITION Moving by 0.040870 0.441520 0.052998
>
> NSTEP = 20000 TIME(PS) = 10.000 TEMP(K) = 11.43 PRESS =
> 0.0
> Etot = -8575.9895 EKtot = 93.0162 EPtot =
> -8669.0057
> BOND = 134.8024 ANGLE = 462.2500 DIHED =
> 2215.2976
> 1-4 NB = 649.7273 1-4 EEL = 7919.3754 VDWAALS =
> -1791.1755
> EELEC = -14836.4375 EGB = -3422.8453 RESTRAINT =
> 0.0000
> ------------------------------------------------------------------------------
>
>
> A V E R A G E S O V E R 20000 S T E P S
>
>
> NSTEP = 20000 TIME(PS) = 10.000 TEMP(K) = 6.77 PRESS =
> 0.0
> Etot = -8649.1636 EKtot = 55.1012 EPtot =
> -8704.2648
> BOND = 126.2944 ANGLE = 439.5599 DIHED =
> 2217.1735
> 1-4 NB = 648.2991 1-4 EEL = 7915.4244 VDWAALS =
> -1792.9242
> EELEC = -14941.3298 EGB = -3316.7621 RESTRAINT =
> 0.0000
> ------------------------------------------------------------------------------
>
>
> R M S F L U C T U A T I O N S
>
>
> NSTEP = 20000 TIME(PS) = 10.000 TEMP(K) = 3.11 PRESS =
> 0.0
> Etot = 43.9817 EKtot = 25.2987 EPtot =
> 19.1895
> BOND = 5.4996 ANGLE = 13.4675 DIHED =
> 4.0147
> 1-4 NB = 2.0976 1-4 EEL = 6.1379 VDWAALS =
> 4.2862
> EELEC = 72.7734 EGB = 71.7080 RESTRAINT =
> 0.0000
> ------------------------------------------------------------------------------
>
> and the input file was:
>
> Stage 1 heating of Endonuc 0 to 100K
> &cntrl
> imin=0, irest=0, ntx=1,
> nstlim=20000, dt=0.0005,
> ntc=2, ntf=2,
> ntt=3, ig=-1,gamma_ln=0.01,
> tautp=1.0,
> tempi=0.0, temp0=100.0,
> ntpr=50, ntwx=50,
> ntb=0, igb=1,
> cut=999.,rgbmax=999.
> /
>
> The molecule is a protein, 200 aa long.
> Could you please explain me why the desired temperature hasn't been reached?
>
> Kind regards,
> Nick
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Received on Tue Nov 01 2016 - 11:00:04 PDT
