In cases like this, a quick flail is often more revealing than reasoned
reading of the manual followed by meditation and a dive into the code,
so what if you try
a) setting tempi=0 (see manual)
b) setting temp0 in the main part, just in case the code expects it
c) remove the warming and cold-start at 300K just to see what happens,
my 1st idea
Bill
On 6/2/19 2:07 AM, Vaibhav Dixit wrote:
> Dear All,
> I am heating up a minimized system (CYP450
> <http://archive.ambermd.org/201905/0331.html>) in the implicit solvent with
> 473 residues.
> The mdout_analyzer.py heat.out graph attached shows that the temperature is
> not rising above 60K. I took the input template from consph tutorial here
> <http://ambermd.org/tutorials/advanced/tutorial18/section2.htm>.
> I ran another longer simulation assuming that it would let the temp rise to
> target 300 K, but this doesn't seem to have happened.
> Can you please check/suggest what mistake am making, in either reading the
> out file or setting the input files?
> My PBS script is given below for reference.
> I briefly read the "17.6.7. Temperature regulation" section, but not being
> an expert couldn't quickly understand the reason for temp not moving above
> 60K.
>
> [r11831vd.hlogin1 [csf3] 3A4-implicit-sol]$ tail heat2.out
> NSTEP = 1500 TIME(PS) = 3.000 *TEMP(K) = 60.86* PRESS =
> 0.0
> Etot = -13864.3602 EKtot = 1170.9430 EPtot =
> -15035.3033
> BOND = 516.2669 ANGLE = 1670.5681 DIHED =
> 4835.1562
> 1-4 NB = 1616.9575 1-4 EEL = 18935.0265 VDWAALS =
> -4329.3383
> EELEC = -31874.0368 EGB = -6477.3909 RESTRAINT =
> 71.4875
> EAMBER (non-restraint) = -15106.7907
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
> ===============================================================================
> [r11831vd.hlogin1 [csf3] 3A4-implicit-sol]$
>
> heat2.in
> ---------------------
> Implicit solvent constant pH initial heating mdin
> &cntrl
> imin=0, irest=0, ntx=1,
> ntpr=500, ntwx=500, nstlim=10000000,
> dt=0.002, ntt=3, tempi=60,
> temp0=300, tautp=2.0, ig=-1,
> ntp=0, ntc=2, ntf=2, cut=30,
> ntb=0, igb=2, tol=0.000001,
> nrespa=1, saltcon=0.1, icnstph=1,
> ntcnstph=100000000,
> gamma_ln=5.0, ntwr=500, ioutfm=1,
> nmropt=1, ntr=1, restraint_wt=2.0,
> restraintmask='.CA,C,O,N',
> /
> &wt
> TYPE='TEMP0', ISTEP1=1, ISTEP2=500000,
> VALUE1=60.0, VALUE2=300.0,
> /
> &wt TYPE='END' /
>
> PBS script
> [r11831vd.hlogin1 [csf3] 3A4-implicit-sol]$ more amber-heat
> #!/bin/bash --login
> #$ -cwd
> #$ -pe smp.pe 24
> # Load the software
> module load apps/intel-17.0/amber/18-at19-may2019
>
> mpirun -n $NSLOTS sander.MPI -O -i heat2.in -o heat2.out -c
> P450-1W0E-gas-heat.rst7 -r P450-1W0E-gas-heat2.rst7 -p P450-1W0E-gas.prmtop
> -
> ref P450-1W0E-gas-heat.rst7 -cpin P450-1W0E-gas-min.cpin -x
> P450-1W0E-gas-heat2.nc -cpout P450-1W0E-gas-heat2.cpout
>
> [r11831vd.hlogin1 [csf3] 3A4-implicit-sol]$
>
>
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Received on Sun Jun 02 2019 - 05:30:02 PDT
