Note this cryptic line:
NITER, NIT, LL, I and J are : 0 0 6453 12957 12960
This indicates that atoms 12957 and 12960 are probably on top of each
other - save coordinates each step, and watch the animation for further
clues.
Bill
On 8/1/17 9:49 AM, Alonso Martinez, Diego wrote:
> Dear Carlos,
>
> I did the simulation with a simple CPU core. The result is the following:
>
> NSTEP = 67 TIME(PS) = 0.134 TEMP(K) = 240.67 PRESS = 0.0
> Etot = -390163.0338 EKtot = 68353.4008 EPtot = -458516.4347
> BOND = 2933.8606 ANGLE = 5886.9228 DIHED = 11730.6656
> 1-4 NB = 3292.7434 1-4 EEL = 24119.9842 VDWAALS = 54763.1248
> EELEC = -561243.7361 EHBOND = 0.0000 RESTRAINT = 0.0000
> Ewald error estimate: 0.2413E-03
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
> ===============================================================================
> vlimit exceeded for step 67; vmax = 95.1582
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 0 6453 12957 12960
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
>
>
> Do you have any comment about how to proceed to solve this issue from the information in this email and the previous? Many thanks.
>
> Best wishes,
> Diego
>
>
>
> On 01/08/2017, 15:54, "Carlos Simmerling" <carlos.simmerling.gmail.com> wrote:
>
> try doing this with a single CPU core and not using MPI. it tends to be
> better at writing error messages to the mdout file.
>
> On Tue, Aug 1, 2017 at 10:48 AM, Alonso Martinez, Diego <
> diego.alonso-martinez12.imperial.ac.uk> wrote:
>
> > Dear Amber users,
> >
> > Bill, many thanks for your help.
> >
> > I’ve tried to run 10K dynamics without restraints to relax the things as
> > you proposed. To do so, after running the minimization as before, I run a
> > heating step from 0 to 10 K followed by a 10K run. However, instead of just
> > heating to 10K, the temperature keeps on rising gradually reaching 240.41K
> > instead of the requested 10K, at which point it stops.
> >
> > I forgot to mention that the structure is formed by protein subunits each
> > derived from an homology model and put together based on an homologous
> > protein complex. I wonder if the issue is that I have bad contacts in the
> > initial structure and if so how to fix it.
> >
> > The script I used to do the heating during 500 ps from 0 to 10K with no
> > restraints was:
> >
> > &cntrl
> > imin=0,
> > irest=0,
> > ntx=1,
> > nstlim=250000, dt=0.002, ntc=2,
> > ntf=2,
> > tol=0.0000001,
> > cut=10.0,
> > ntb=1,
> > ntpr=1,
> > ntwx=1,
> > ntt=3,
> > gamma_ln=1.0,
> > ig=-1,
> > ntr=0,
> > ntp=0,
> > ioutfm=1, nmropt=1,
> > ntxo=2,
> > /
> > &wt TYPE='TEMP0', istep1=0, istep2=250000,
> > value1=0.0, value2=10.0 /
> > &wt TYPE='END' /
> >
> > The output of the first step was:
> >
> > NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
> > 0.0
> > Etot = -377171.6447 EKtot = 0.0000 EPtot =
> > -377171.6447
> > BOND = 21999.6885 ANGLE = 5590.9971 DIHED =
> > 11036.2669
> > 1-4 NB = 4130.5966 1-4 EEL = 25899.7724 VDWAALS =
> > 22637.8494
> > EELEC = -468466.8157 EHBOND = 0.0000 RESTRAINT =
> > 0.0000
> > Ewald error estimate: 0.9785E-03
> > ------------------------------------------------------------
> > ------------------
> >
> > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
> >
> >
> > Whereas the last step after which the simulation stopped was:
> >
> > NSTEP = 65 TIME(PS) = 0.130 TEMP(K) = 240.41 PRESS =
> > 0.0
> > Etot = -389058.7206 EKtot = 68279.1807 EPtot =
> > -457337.9013
> > BOND = 3093.9788 ANGLE = 6161.3515 DIHED =
> > 11719.1974
> > 1-4 NB = 3272.8328 1-4 EEL = 24198.5591 VDWAALS =
> > 54660.9222
> > EELEC = -560444.7431 EHBOND = 0.0000 RESTRAINT =
> > 0.0000
> > Ewald error estimate: 0.2856E-03
> > ------------------------------------------------------------
> > ------------------
> >
> > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
> > ============================================================
> > ===================
> >
> > Do you have any input about the reason why you think this is happening?
> >
> > Any input is welcome. Many thanks for your help.
> >
> > Diego
> >
> >
> >
> >
> > On 20/07/2017, 21:00, "Bill Ross" <ross.cgl.ucsf.edu> wrote:
> >
> > If you do as I advise, you might immediately see what the problem is.
> >
> > Bill
> >
> > <div>-------- Original message --------</div><div>From: "Alonso
> > Martinez, Diego" <diego.alonso-martinez12.imperial.ac.uk>
> > </div><div>Date:07/20/2017 12:33 PM (GMT-08:00) </div><div>To: AMBER
> > Mailing List <amber.ambermd.org> </div><div>Subject: Re: [AMBER] Sander
> > doing the minimisation but stopping at the first
> > heating step, not generating rst or nc files </div><div>
> > </div>Dear all,
> >
> > Many thanks for your time and help.
> >
> > The system had already undergone minimisation before I started this
> > heating run. Perhaps I didn’t choose the adequate parameters for
> > minimization or it is not sufficient? The two round of minimization that I
> > used for this system were:
> >
> > Round #1:
> > Minimise complex with 2 kcal mol restraints in 10000 steps
> > &cntrl
> > imin=1,maxcyc=10000,ncyc=3000,
> > cut=12.0,ntb=1,
> > ntc=2,ntf=2,
> > ntpr=100,
> > ntr=1,
> > /
> > Allowing only water and the counterions to move with 2 kcal mol
> > restraint
> > 2.0
> > RES 1 857
> > END
> > END
> >
> > Round #2:
> > Minimise complex with no restraints
> > &cntrl
> > imin=1,maxcyc=10000,ncyc=3000,
> > cut=12.0,ntb=1,
> > ntc=2,ntf=2,
> > ntpr=100,
> > ntr=0,
> > /
> >
> > Please let me know if you have any further inputs. Many thanks.
> >
> > Best wishes,
> > Diego
> >
> >
> >
> > On 20/07/2017, 20:23, "Bill Ross" <ross.cgl.ucsf.edu> wrote:
> >
> > I would try running plain 10K dynamics without restraints to relax
> > things. View the trajectory, and you might see where the problem
> > is with
> > your restrained model.
> >
> > Bill
> >
> >
> > On 7/20/17 12:19 PM, Alonso Martinez, Diego wrote:
> > > Dear all,
> > >
> > > In addition to what I previously described, the following
> > information also appeared:
> > >
> > > vlimit exceeded for step 40; vmax = 33.6600
> > >
> > > Coordinate resetting (SHAKE) cannot be accomplished,
> > > deviation is too large
> > > NITER, NIT, LL, I and J are: 0 0 6457 12945
> > 12946
> > >
> > > Note: This is usually a symptom of some deeper
> > > problem with the energetics of the system.
> > >
> > > Best wishes,
> > > Diego
> > >
> > > On 20/07/2017, 19:58, "Alonso Martinez, Diego" <
> > diego.alonso-martinez12.imperial.ac.uk> wrote:
> > >
> > > Dear all,
> > >
> > > Many thanks for your inputs.
> > >
> > > I’ve followed your recommendations. The simulation now runs
> > up to 40 steps where it stops. The output for step 0 is:
> > >
> > > NSTEP = 0 TIME(PS) = 0.000 TEMP(K) =
> > 0.00 PRESS = 0.0
> > > Etot = -377171.9116 EKtot = 0.0000 EPtot
> > = -377171.9116
> > > BOND = 22001.3894 ANGLE = 5591.1333 DIHED
> > = 11036.2664
> > > 1-4 NB = 4130.6427 1-4 EEL = 25899.8412
> > VDWAALS = 22638.7966
> > > EELEC = -468469.9812 EHBOND = 0.0000
> > RESTRAINT = 0.0000
> > > Ewald error estimate: 0.9785E-03
> > > ------------------------------
> > ------------------------------------------------
> > >
> > > NMR restraints: Bond = 0.000 Angle = 0.000
> > Torsion = 0.000
> > >
> > >
> > > And the output for the last step (40) is:
> > >
> > > NSTEP = 40 TIME(PS) = 0.080 TEMP(K) =
> > 158.88 PRESS = 0.0
> > > Etot = -382330.0469 EKtot = 45123.8992 EPtot
> > = -427453.9461
> > > BOND = 8652.6936 ANGLE = 4998.5073 DIHED
> > = 11097.1310
> > > 1-4 NB = 3798.8621 1-4 EEL = 25049.1304
> > VDWAALS = 47662.3745
> > > EELEC = -542003.8679 EHBOND = 0.0000
> > RESTRAINT = 13291.2230
> > > EAMBER (non-restraint) = -440745.1691
> > > Ewald error estimate: 0.5425E-03
> > > ------------------------------
> > ------------------------------------------------
> > >
> > > NMR restraints: Bond = 0.000 Angle = 0.000
> > Torsion = 0.000
> > >
> > >
> > > What surprised me the most about this outcome is the fact
> > that I set the temperature to increase from 0 to 100 K but it does increase
> > up to 158.88K. Do you have any input about why this could be happening?
> > Many thanks.
> > >
> > > Best wishes,
> > > Diego
> > >
> > >
> > > On 20/07/2017, 14:40, "Carlos Simmerling" <
> > carlos.simmerling.gmail.com> wrote:
> > >
> > > also run with single thread, not MPI.
> > >
> > > On Thu, Jul 20, 2017 at 9:22 AM, Adrian Roitberg <
> > roitberg.ufl.edu> wrote:
> > >
> > > > Try setting ntpr=1 and ntwx=1 and see if you ever go
> > beyond the first
> > > > step and what happens.
> > > >
> > > > Right now you have them set to 5000, so lots of
> > things could have
> > > > happened between those steps.
> > > >
> > > > adrian
> > > >
> > > >
> > > > On 7/20/17 9:05 AM, Alonso Martinez, Diego wrote:
> > > > > Dear Amber users,
> > > > >
> > > > > I am trying to obtain a MD trajectory of a
> > DNA-protein-metal-ligand
> > > > complex.
> > > > >
> > > > > To prepare the inpcrd and prmtop files, I followed
> > the following
> > > > approach: first, I’ve prepared PDB files of each of
> > the elements of the
> > > > simulation: the protein and the DNA with the H++
> > webserver, the ligand and
> > > > metal with antechamber. Then, I joined all the pdb
> > files into one with the
> > > > cat command, to then generate the inpcrd and prmtop
> > files of the complex
> > > > with tleap.
> > > > >
> > > > > The tleap input file was as follows:
> > > > >
> > > > > source leaprc.protein.ff14SB
> > > > > source leaprc.DNA.OL15
> > > > > source leaprc.water.tip3p
> > > > > source leaprc.gaff2
> > > > > CPF = loadmol2 CPF.mol2
> > > > > loadamberparams CPF.frcmod
> > > > > loadamberparams frcmod.ions234lm_126_tip3p
> > > > > mol = loadpdb Gyrase_complex_fixed.pdb
> > > > > savepdb mol Gyrase_complex_dry.pdb
> > > > > saveamberparm mol Gyrase_complex_dry.prmtop
> > Gyrase_complex_dry.inpcrd
> > > > > solvateoct mol TIP3PBOX 15.0
> > > > > addions mol Na+ 0
> > > > > addions mol Cl- 0
> > > > > savepdb mol Gyrase_complex_solv.pdb
> > > > > saveamberparm mol Gyrase_complex_solv.prmtop
> > Gyrase_complex_solv.inpcrd
> > > > > quit
> > > > >
> > > > > The method used to parametrize the metal ion is the
> > nonbonded model as
> > > > we want to observe if the metal ion exits the binding
> > site upon mutations
> > > > in the protein. The parametrization was checked with
> > parmed.
> > > > >
> > > > > Inpcrd and prmtop files of the solvated complex
> > were then generated.
> > > > Then, we proceeded with an energy minimization using
> > sander.MPI, followed
> > > > by heating with sander.MPI as well. The minimization
> > run fine, at least
> > > > when compared to previously successful minimizations.
> > However, when it
> > > > passed to the heating, the mdout file only prints the
> > first step and does
> > > > not continue the simulation after that, not even
> > generating a trajectory
> > > > file. The mdout file was:
> > > > >
> > > > > NSTEP = 0 TIME(PS) = 0.000 TEMP(K)
> > = 0.00 PRESS =
> > > > 0.0
> > > > > Etot = -393779.1731 EKtot =
> > 0.0000 EPtot =
> > > > -393779.1731
> > > > > BOND = 23619.4348 ANGLE =
> > 5814.7119 DIHED =
> > > > 11047.5656
> > > > > 1-4 NB = 4193.6173 1-4 EEL =
> > 25963.2849 VDWAALS =
> > > > 29449.7359
> > > > > EELEC = -493867.5237 EHBOND =
> > 0.0000 RESTRAINT =
> > > > 0.0000
> > > > > Ewald error estimate: 0.7721E-03
> > > > > NMR restraints: Bond = 0.000 Angle =
> > 0.000 Torsion =
> > > > 0.000
> > > > > ==============================
> > ==============================
> > > > ===================
> > > > >
> > > > > After which no more steps are printed. The program
> > just exits and
> > > > doesn’t generate trajectory or restart files to
> > continue to the next
> > > > heating step. The heating input file was:
> > > > >
> > > > > &cntrl
> > > > > imin=0,
> > > > > irest=0,
> > > > > ntx=1,
> > > > > nstlim=250000, dt=0.002,
> > > > > ntc=2, ntf=2,
> > > > > tol=0.0000001,
> > > > > cut=10.0, ntb=1,
> > > > > ntpr=5000, ntwx=5000,
> > > > > ntt=3, gamma_ln=1.0,
> > > > > ig=-1,
> > > > > ntr=1,
> > > > > ntp=0,
> > > > > ioutfm=1,
> > > > > nmropt=1,
> > > > > ntxo=2,
> > > > > /
> > > > > &wt TYPE='TEMP0', istep1=0, istep2=250000,
> > > > > value1=0.0, value2=100.0 /
> > > > > &wt TYPE='END' /
> > > > > Hold protein and ligand fixed
> > > > > 10.0
> > > > > RES 1 857
> > > > > END
> > > > > END
> > > > >
> > > > > I’ve tried fixing this issue by removing the energy
> > constraints and
> > > > changing sander for pmemd but none of these options
> > work. Could you please
> > > > let me know if you had any issue like this and if so
> > propose possible
> > > > solutions? Many thanks for your help.
> > > > >
> > > > > Best wishes,
> > > > > Diego
> > > > >
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > > --
> > > > Dr. Adrian E. Roitberg
> > > > University of Florida Research Foundation Professor
> > > > Department of Chemistry
> > > > University of Florida
> > > > roitberg.ufl.edu
> > > > 352-392-6972
> > > >
> > > >
> > > > _______________________________________________
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> > >
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Received on Tue Aug 01 2017 - 11:30:04 PDT
