Hi Christina,
ntr=1 sets positional (Cartesian) restraints. I do no think that
NMR weight changes will affect these.
Cheers,
Hannes.
On Mon, 18 May 2015 09:05:09 -0600
Christina Bergonzo <cbergonzo.gmail.com> wrote:
> Hi Juan,
>
> Everyone else's comments in this discussion are accurate.
>
> But to answer your question, you should be able to change the weights
> of the positional restraints and the temperature using the same input
> file. This is probably most often done in NMR refinement, and you can
> reference the tutorial for that as well:
> http://ambermd.org/tutorials/advanced/tutorial4/
> I have tested this (quickly) in the serial versions of sander and
> pmemd. The way to do this is to switch to using older-style weight
> restraints instead of the group restraint input.
>
> Here is an example:
>
> Test run
> &cntrl
> ntpr = 10, ntwr = 500, ntwx = 500, ntwe = 500,
> ntf = 2, ntc = 2, ntb = 1, ntp = 0, nscm = 500,
> ntt = 3, ig=-1, gamma_ln=1.0,
> tautp = 0.5, taup = 5.0, cut = 9.0,
> nstlim = 2000, dt = 0.002, iwrap = 1,
> irest = 0,* ntr=1, restraint_wt = 500.0,*
> * restraintmask = "!:WAT & !.H=",*
> ntx = 1, tol = 0.00000001, ioutfm=1,
> nmropt=1, tempi=300.0,
> /
> &wt type = 'REST', istep1=0,istep2=750,value1=0.08,value2=0.08, /
> &wt type = 'REST', istep1=751,istep2=1000,value1=0.08,value2=1.0, /
> &wt type = 'REST', istep1=1001,istep2=2000,value1=1.0,value2=1.0, /
> &wt type='TEMP0', istep1=0, istep2=500, value1=300.0,
> value2=700.0, / &wt type='TEMP0', istep1=501, istep2=1000,
> value1=700.0, value2=700.0, / &wt type='TEMP0', istep1=1001,
> istep2=2000, value1=700.0, value2=300.0, / &wt type = 'END', /
> &end
>
> Hope this is helpful,
>
> Christina
>
> On Mon, May 18, 2015 at 6:06 AM, Juan Eiros Zamora <
> j.eiros-zamora14.imperial.ac.uk> wrote:
>
> > Hi everyone,
> >
> > I am trying to replicate an MD protocol that has been done
> > previously using NAMD 2.9 using AMBER.
> >
> > After the initial minimisation steps (water and ions, then backbone
> > of protein and so on), I am trying to do the following:
> >
> > "380 ps initial MD run with consecutively weaker restraints on
> > protein atoms and gradually heat up the system to 300K"
> >
> > Usually in my minimisation input file I keep the restraints constant
> > like this:
> > > Stage 1 - 1000 step minimisation of water and ions
> > > &cntrl
> > > imin=1, maxcyc=1000, ncyc=500,
> > > cut=12.,ntb=1,ntr=1,
> > > ntpr=100
> > > /
> > > Hold protein fixed
> > > 500.0
> > > RES 1 422
> > > END
> > > END
> >
> > And to heat up a system I do it like this (after the &cntrl
> > section):
> >
> > > &wt type='TEMP0', istep1=0, istep2=50000,
> > > value1=0.0, value2=300.0 /
> > > &wt type='END' /
> > > Hold protein fixed
> > > 10.0
> > > RES 1 422
> > > END
> > > END
> >
> > Does anyone have an idea of how could I change two variables at a
> > time? I've looked into section 18.8 of the Manual, but I am not
> > sure if I should change the BOND option or the REST one, or how to
> > proceed to change one of the two as well as the TEMP0 option.
> >
> > Looking forward to hear any suggestion on this matter,
> >
> > Juan
> >
> >
> > _______________________________________________
> > 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
Received on Mon May 18 2015 - 09:00:04 PDT
