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
>
--
---------------------------------------------------------------------------------------
Christina Bergonzo, PhD
Postdoctoral Researcher
Department of Medicinal Chemistry, University of Utah
30 South 2000 East, Rm. 201
Salt Lake City, UT 84112-5820
Office: L.S. Skaggs Pharmacy Research Institute, Rm.4290
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652 / Fax: (801) 585-6208
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Received on Mon May 18 2015 - 08:30:03 PDT
