I've been running equilibrations using sander (MPI), then I switch to pmemd
for production runs. Maybe run md1 (which is a 3 ns equilibration) using
sander (MPI)?
Best Regards,
Andrew
On Sat, Apr 23, 2016 at 11:30 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> You could try dropping you starting temperature further, even to 1. I
> would also save every frame, and watch the animation for clues.
>
> Bill
>
> On 4/23/16 2:49 AM, Takuya Uto wrote:
> > Thank you for your suggestion.
> >
> > Although I have tried to do the calculations in NTV it does not work.
> >
> > The input file and out file is shown below .
> >
> > I use GPU Version of PMEMD.cuda module.
> >
> > I understand that the equilibration process is bad as you pointed out.
> >
> > However , I do not know whether any protocol is good . Please help me.
> >
> >
> >
> > Best regards.
> >
> > Takuya Uto
> >
> >
> >
> > #### md input ######################
> >
> > molecular dynamics
> >
> > &cntrl
> >
> > imin = 0, irest = 0, ntx = 1,
> >
> > ntb = 1, cut = 14.0 , iwrap = 0,
> >
> > ntt = 3, gamma_ln = 5.0 ,
> >
> > tempi = 20.0, temp0 = 20.0,
> >
> > nstlim = 1000000, dt = 0.0001,
> >
> > ntpr = 100, ntwx = 100, ntwr = 100,
> >
> > &end
> >
> > ##################################
> >
> >
> >
> > NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 20.00 PRESS =
> > 0.0
> >
> > Etot = -2459.3191 EKtot = 125.2190 EPtot =
> > -2584.5381
> >
> > BOND = 25.7564 ANGLE = 729.3448 DIHED =
> > 74.6309
> >
> > 1-4 NB = 71.3685 1-4 EEL = -517.5268 VDWAALS =
> > -424.0162
> >
> > EELEC = -2544.0957 EHBOND = 0.0000 RESTRAINT =
> > 0.0000
> >
> >
> ----------------------------------------------------------------------------
> > --
> >
> >
> >
> >
> >
> > NSTEP = 100 TIME(PS) = 0.010 TEMP(K) =********* PRESS =
> > 0.0
> >
> > Etot = ************** EKtot = ************** EPtot =
> > **************
> >
> > BOND = ************** ANGLE = 208168.0251 DIHED =
> > 7293.6233
> >
> > 1-4 NB = -0.0000 1-4 EEL = -0.0876 VDWAALS =
> > **************
> >
> > EELEC = -2395.0676 EHBOND = 0.0000 RESTRAINT =
> > 0.0000
> >
> >
> ----------------------------------------------------------------------------
> > --
> >
> >
> >
> >
> >
> > NSTEP = 200 TIME(PS) = 0.020 TEMP(K) =********* PRESS =
> > 0.0
> >
> > Etot = ************** EKtot = ************** EPtot =
> > **************
> >
> > BOND = ************** ANGLE = 144728.1573 DIHED =
> > 7627.9577
> >
> > 1-4 NB = 0.0000 1-4 EEL = -0.1720 VDWAALS =
> > **************
> >
> > EELEC = -1513.7364 EHBOND = 0.0000 RESTRAINT =
> > 0.0000
> >
> >
> ----------------------------------------------------------------------------
> > --
> >
> >
> >
> >
> >
> > From: Takuya Uto [mailto:t.uto.cc.miyazaki-u.ac.jp]
> > Sent: Saturday, April 23, 2016 6:29 PM
> > To: 'Takuya Uto' <t.uto.cc.miyazaki-u.ac.jp
> > <mailto:t.uto.cc.miyazaki-u.ac.jp> >
> > Subject:
> >
> >
> >
> > From: kurisaki <kurisaki.ncube.human.nagoya-u.ac.jp
> > <mailto:kurisaki.ncube.human.nagoya-u.ac.jp
> ?Subject=Re%3A%20%5BAMBER%5D%20Ho
> > w%20to%20deal%20with%20monoatomic%20ion%2C%20such%20as%20ILs%20anion> >
> > Date: Fri, 22 Apr 2016 10:57:39 +0900
> >
> >
> > Before you execute production runs,
> > How about relaxing the system more carefully?
> > For example, use a smaller integration steps (0.01 ps)
> > and NVT simulation:
> > NPT simulation might make steric crash
> > and cause anomalous energy raise,
> > If the system is not sufficiently 'relaxed'.
> >
> > My best,
> >
> > IK
> >
> >
> >
> > From: Bill Ross <
> > <mailto:ross.cgl.ucsf.edu
> ?Subject=Re%3A%20%5BAMBER%5D%20How%20to%20deal%20wi
> > th%20monoatomic%20ion%2C%20such%20as%20ILs%20cation> ross.cgl.ucsf.edu>
> > Date: Thu, 21 Apr 2016 18:39:21 -0700
> >
> >
> > What is the error you encountered? I suggest posting the text and your
> > md input.
> >
> > Usually such complaints are due to bad equilibration protocols.
> >
> > Bill
> >
> > On 4/21/16 6:29 PM, Takuya Uto wrote:
> >> Dear Sir
> >>
> >>
> >>
> >> Currently , I try the simulation using the typical ionic liquid, such as
> >> [BMIM][Cl] etc...
> >>
> >> It has followed the TUTORIAL A15. LEaP and minimization works are going
> >> well.
> >>
> >> But, I have encountered an error in the MD calculation.
> >>
> >> I have it two points that you want to ask .
> >>
> >> 1. Is it difficult for AMBER software to calculate a large number of
> >> monoatomic ion.
> >>
> >> 2. Cl- parameters were applied parameters of Li et al . Is this wrong ?
> >>
> >>
> >>
> >> Regards.
> >>
> >> Takuya Uto
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 24.24 PRESS =
> >> 0.0
> >>
> >> Etot = -2461.6391 EKtot = 125.2190 EPtot =
> >> -2586.8582
> >>
> >> BOND = 22.7264 ANGLE = 729.3448 DIHED =
> >> 74.6309
> >>
> >> 1-4 NB = 71.3685 1-4 EEL = -517.5268 VDWAALS =
> >> -423.1190
> >>
> >> EELEC = -2544.2829 EHBOND = 0.0000 RESTRAINT =
> >> 0.0000
> >>
> >>
> >
> ----------------------------------------------------------------------------
> >
> >> --
> >>
> >>
> >>
> >>
> >>
> >> NSTEP = 500 TIME(PS) = 1.000 TEMP(K) =********* PRESS =
> >> 0.0
> >>
> >> Etot = ************** EKtot = ************** EPtot =
> >> **************
> >>
> >> BOND = -0.0000 ANGLE = 184688.7258 DIHED =
> >> 7322.8481
> >>
> >> 1-4 NB = 0.0000 1-4 EEL = 0.0003 VDWAALS =
> >> **************
> >>
> >> EELEC = -2577.3284 EHBOND = 0.0000 RESTRAINT =
> >> 0.0000
> >>
> >>
> >
> ----------------------------------------------------------------------------
> >
> >> --
> >>
> >>
> >>
> >>
> >>
> >> NSTEP = 1000 TIME(PS) = 2.000 TEMP(K) =********* PRESS =
> >> 0.0
> >>
> >> Etot = ************** EKtot = ************** EPtot =
> >> **************
> >>
> >> BOND = -0.0000 ANGLE = 188853.5435 DIHED =
> >> 7524.3485
> >>
> >> 1-4 NB = 0.0000 1-4 EEL = 0.0001 VDWAALS =
> >> **************
> >>
> >> EELEC = -1385.1898 EHBOND = 0.0000 RESTRAINT =
> >> 0.0000
> >>
> >>
> >
> ----------------------------------------------------------------------------
> >
> >> --
> >>
> >> _______________________________________________
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> >> AMBER.ambermd.org
> >> <http://lists.ambermd.org/mailman/listinfo/amber>
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
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>
>
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--
Andrew Schaub
Graduate Program in Chemical & Structural Biology
Tsai Lab, http:///www.tsailabuci.com/ <http://www.tsailabuci.com/>
Luo Lab, http://rayl0.bio.uci.edu/html/
University of California, Irvine
Irvine, CA 92697-2280
949-824-8829 (lab)
949-877-9380 (cell)
aschaub.uci.edu <http://www.linkedin.com/pub/andrew-schaub/9a/907/382/>
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Received on Sat Apr 23 2016 - 12:00:05 PDT
