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,
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?
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
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Aug 12 2015 - 07:00:04 PDT
