Duh, I missed that you are apparently restraining your backbone!
restraint_wt=2.0,
restraintmask='.CA,C,O,N',
That would be like doing the Lambada in an iron lung, as far as allowing any heat to occur. You want a flexible spine, and sensitive touch, not checking in every 500 steps:
ntpr=500
Bill
On 6/2/19 5:00 AM, Bill Ross wrote:
>
> 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
