On Wed, Aug 12, 2015 at 9:34 AM, Amber mail <amber.auc14.gmail.com> wrote:
> Dear Jason
>
> Many Thanks.. this really helps!
>
> I am just wondering that the results was looking good, and it was not weird
> !
>
> One more question regarding the Temperature and Pressure regulation, I used
> tautp=1.0,
>
>
tautp has no effect when ntt=3. It is only used for ntt=1 (and I
recommend *against* using ntt=1 for anything).
>
> taup=1.0 and pres0=1.01325 for the first heating stage and the remaining
>
> stages as shown below in the control file, but not for the MD production.
>
> Does this result in unwanted perturbation or something goes wrong in the
>
> system?
>
Nothing looks wrong at a quick glance, but I certainly could have missed
something.
Good luck,
Jason
>
> Heat (0-100)K
> > &cntrl
> > imin=0,
> > ntx=1,
> > irest=0,
> > nstlim=25000,
> > dt=0.002,
> > ntf=2,
> > ntc=2,
> > tempi=0.0,
> > temp0=100.0,
> > ntpr=100,
> > ntwx=100,
> > cut=8.0,
> > ntb=2,
> > ntp=1,
> > ntt=3,
> > gamma_ln=1.0,
>
> nmropt=0,
>
> tautp=1.0,
> > taup=1.0,
> > pres0=1.01325,
> > ig=-1,
> > iwrap=1,
> > /
> >
>
> Production
> > &cntrl
> > imin=0,
> > ntx=5,
> > irest=1,
> > nstlim=5000000,
> > dt=0.002,
> > ntf=2,
> > ntc=2,
> > temp0=310.0,
> > tempi=310.0,
> > ntpr=5000,
> > ntwx=5000,
> > cut=8.0,
> > ntb=2,
> > ntp=1,
> > ntt=3,
> > gamma_ln=1.0,
>
> nmropt=0,
> > ig=-1,
> > iwrap=1,
> > /
> >
>
> Best Regards
>
> On Wed, Aug 12, 2015 at 12:00 AM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
> > On Tue, Aug 11, 2015 at 4:53 PM, Amber mail <amber.auc14.gmail.com>
> wrote:
> >
> > > Dear Adrian and Daniel,
> > >
> > > Thanks a lot.. I really appreciate it !
> > >
> > > I was wondering if you could review my control files to double check
> them
> > > before starting over !
> > > I have finished few introductory tutorials, and I encountered many
> errors
> > > during this run. Please let me know if this possible !
> > >
> >
> > I
> > think this thread is evidence that our double-checking is error-prone.
> > Adrian caught that your input file was missing ig=-1, but I missed that
> > (as I'm sure others would as well). When I first started, I used the
> > manual as a resource for learning about the different input variables and
> > what they meant. It took a few weeks of doing tutorials and reading the
> > relevant sections of the manual before I learned what a lot (most?) of
> them
> > were.
> >
> > You can see the set of input files I usually use for my simulations on
> > Github, hopefully they can be of help to you (notice that they all have
> > ig=-1, for the abovementioned reasons ;)).
> >
> > https://github.com/swails/Mdins
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> > _______________________________________________
> > 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
>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Aug 12 2015 - 07:00:08 PDT
