Hi All,
In the explicit solvent simulation, I'm not getting the same problem and
getting expected temp settle at 300K (see output below).
Strangely while trying Bill's suggestions I'm getting an error message from
PBS that seems not related to Amber programs, but please let me know if you
know the fix.
Thank you for your comments/suggestions.
Explicit solvent (water) heat-simulation output:
[r11831vd.hlogin1 [csf3] 3A4-explicit-sol]$ grep TEMP heat.out | tail -5
NSTEP = 1480000 TIME(PS) = 2960.000 TEMP(K) = 304.57 PRESS =
0.0
NSTEP = 1490000 TIME(PS) = 2980.000 TEMP(K) = 300.43 PRESS =
0.0
NSTEP = 1500000 TIME(PS) = 3000.000 TEMP(K) = 301.23 PRESS =
0.0
NSTEP = 1500000 TIME(PS) = 3000.000 TEMP(K) = 270.99 PRESS =
0.0
NSTEP = 1500000 TIME(PS) = 3000.000 TEMP(K) = 69.08 PRESS =
0.0
.
ERROR message from the PBS
----------------
[r11831vd.hlogin1 [csf3] 3A4-implicit-sol]$ tail amber-heat1.e441494
sander.MPI 000000000048E81E main Unknown Unknown
libc-2.17.so 00002B8EBCC55C05 __libc_start_main Unknown Unknown
sander.MPI 000000000048E729 Unknown Unknown Unknown
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status,
thus causing
the job to be terminated. The first process to do so was:
Process name: [[63619,1],0]
Exit code: 24
--------------------------------------------------------------------------
On Sun, Jun 2, 2019 at 1:06 PM Bill Ross <ross.cgl.ucsf.edu> wrote:
> 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 $NSLOTS sander.MPI -O -i heat2.in -o heat2.out -c
> >> P450-1W0E-gas-heat.rst7 -r P450-1W0E-gas-heat2.rst7 -p
> P450-1W0E-gas.prmtop
> >> -
> >> ref P450-1W0E-gas-heat.rst7 -cpin P450-1W0E-gas-min.cpin -x
> >> P450-1W0E-gas-heat2.nc -cpout P450-1W0E-gas-heat2.cpout
> >>
> >> [r11831vd.hlogin1 [csf3] 3A4-implicit-sol]$
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
Assistant Professor,
Department of Pharmacy,
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Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
India.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
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Received on Sun Jun 02 2019 - 09:30:02 PDT
