Let me shamelessly plug my new toy in mdgx: configuration sampling, to be
released in AmberTools v17 after I do a bit more polishing. I'm not using
it for its primary purpose, but it does perform energy minimizations with
array of NMR restraints and thereafter creates a report file containing
information to help identify bad conformations and help the user to see "I
guess it doesn't bend that way!" For this case, I am making use of the
sanity checking. Here's the output:
<++>-----------------------------------------------------------------------<++>
(3.) Basic sanity checks. If a configuration fails these tests, it was not
printed out for further consideration but the reasons it failed will be
summarized here. The tests are that, first, no bond of a configuration
may be strained more than 10.00 kcal/mol. Furthermore, no angle may be
strained more than 10.00 kcal/mol. Finally, the maximum tolerated
restraint energy (summed over all restraints) is 200.00 kcal/mol. If
any
of these tests seem too stringent or not tight enough, the thresholds
may
be changed in the &configs namelist.
- Configurations passing all sanity checks: 0
- Configurations failing bond sanity check: 1
- Configurations failing angle sanity check: 1
- Configurations failing restraint sanity check: 0
Descriptions of each problematic configuration follow, along with the
names and numbers of atoms involved in each feature creating the problem.
- Configuration 1:
Strain is 478.9827 for bond NE -CZ (208, 210)
Strain is 34.6589 for angle NH1 -CZ -NH2 (211, 210, 214)
Restraint binding atoms () strained to 0.0000
<++>-----------------------------------------------------------------------<++>
Look at atoms 208 and 210 in Arg12, I see that, yes, it's stabbed right
through a nearby Phenylalanine.
Dave
On Fri, Jul 15, 2016 at 5:18 PM, Adrian Roitberg <roitberg.ufl.edu> wrote:
> Gerald.
>
> If you share your files we can take a look on my group's side.
>
> We have seen this before due to a VERY weird issue. There are cases
> where tleap decides to create carbon chains going through the middle of
> a phenyl ring for instance. Incredibly enough, some of these are
> perfectly stable at 2 fs, even though they are wrong. 4 fs forces the
> issues and things blow up, but it has nothing to do with the time step,
> it is tleap's fault. I suggest you rerun with 4 fs and ntwx=1, and look
> at your trajectory to see what blows up.
>
>
> Adrian
>
>
>
> On 7/15/16 5:14 PM, Gerald Monard wrote:
> > Hello,
> >
> > On 07/15/2016 09:56 PM, Hai Nguyen wrote:
> >> quick question: have you used ParmEd to change the mass yet?
> >>
> > Yes. I forgot to say: I've modified the topology file with the
> > HMassRepartition command in parmed and I have tested both the "normal"
> > repartioning and the "dowater" option. Same results.
> >
> > Gerald.
> >
> >> Hai
> >>
> >> On Fri, Jul 15, 2016 at 3:54 PM, Gerald Monard <
> >> Gerald.Monard.univ-lorraine.fr> wrote:
> >>
> >>> Hello,
> >>>
> >>> I have a protein system in water (321,300 atoms including ~100,000
> water
> >>> molecules). I'm trying to use Hydrogen Mass Repartitioning (HMR) to
> >>> benefit a 4 fs timestep. However, it seems to fail. dt = 0.002 is OK,
> >>> but with dt = 0.003, the temperature goes bad after a few thousands
> >>> steps, and with dt = 0.004, it's even faster. This is for pmemd.cuda
> >>> with Amber16 (all last patches applied) as well as pmemd.MPI.
> >>>
> >>> The mdin file is:
> >>> &cntrl
> >>> imin = 0, ntx = 5, irest = 1,
> >>> dt = 0.004, nstlim = 1000000,
> >>> ntb = 1,
> >>> ntt = 1, ig = -1, temp0 = 300.,
> >>> ntc = 2,
> >>> ntpr = 1000, ntwx = 10000, ntwv = 00, ntwe = 10000,
> >>> /
> >>>
> >>> From the mdin of the GPU benchmark, I've also tried to add tol =
> >>> 0.000001 as well as ntf = 2. No improvement.
> >>>
> >>> Any idea?
> >>>
> >>> Gerald.
> >>>
> >>> --
> >>>
> >>>
> ____________________________________________________________________________
> >>>
> >>> Prof. Gerald MONARD
> >>> SRSMC, Université de Lorraine, CNRS
> >>> Boulevard des Aiguillettes B.P. 70239
> >>> F-54506 Vandoeuvre-les-Nancy, FRANCE
> >>>
> >>> e-mail : Gerald.Monard.univ-lorraine.fr
> >>> tel. : +33 (0)383.684.381
> >>> fax : +33 (0)383.684.371
> >>> web : http://www.monard.info
> >>>
> >>>
> >>>
> ____________________________________________________________________________
> >>>
> >>>
> >>> _______________________________________________
> >>> 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
> >>
>
> --
> 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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Received on Fri Jul 15 2016 - 15:00:03 PDT
