AMBER Archive (2009)

Subject: Re: [AMBER] slope

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Nov 17 2009 - 05:10:35 CST

I'm not sure what you're asking. does the temperature vs time plot match
what you requested, or not? it sounds fine but you should compare the graph
to your input.

On Mon, Nov 16, 2009 at 11:07 PM, Jio M <jiomm_at_yahoo.com> wrote:

>
> Dear Sir,
>
>
>
>
>
> >the temperature plot should look like what you requested in your input.
>
> >check the mdout file- does sander recognize your request for temperature
>
> >change?
>
>
>
> here is the part of output annealing
>
> #############################
>
> Begin reading energy term weight changes/NMR restraints
>
> WEIGHT CHANGES:
>
> TEMP0 0
> 140000 300.000000 2000.000000
> 0 0
>
> TEMP0 140001 200000 2000.000000
> 2000.000000
> 0 0
>
> TEMP0 200001 340000 2000.000000
> 1000.000000
> 0 0
>
> TEMP0 340001 480000 1000.000000
> 2000.000000
> 0 0
>
> TEMP0 480001 620000 2000.000000
> 1000.000000
> 0 0
>
> TEMP0 620001 760000 1000.000000
> 2000.000000
> 0 0
>
> TEMP0 760001 900000 2000.000000
> 1000.000000
> 0 0
>
> TEMP0 9000011050000 1000.000000
> 300.000000
> 0 0
>
>
>
> RESTRAINTS:
>
>
> ** No restraint defined **
>
>
>
>
> Done reading weight changes/NMR restraints
>
>
>
> I think (please correct me if I am wrong) above indicates temp change.
>
>
>
> Also I plotted graph of Temp vs Time. it seems that the temp
> (y) approx. corresponds to y = mxi + c equation [ where m should
> be one and i is correction factor ,to consider different division
> factor of x and y axis i.e. i = delta y/delta x]
>
>
>
> >note that a temp0 of 2000 will almost certainly give you problems unless
> you
>
> >add additional restraints for things like chirality.
>
> >this is a very high energy state and you can easily get cis-trans
>
> >isomerizations and chirality inversions.
>
>
>
> Actually I have a macromolecule (> 1300 atoms) that donot have
> chiral center or cis trans possibility. But in future I will definately
> consider this while doing high temp annealing, this is nice point to be
> noticed that I didnt know
>
>
>
> thanks and regards;
>
> JIomm
>
>
> --- On Mon, 11/16/09, Carlos Simmerling <carlos.simmerling_at_gmail.com>
> wrote:
>
> From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
> Subject: Re: [AMBER] slope
> To: "AMBER Mailing List" <amber_at_ambermd.org>
> Date: Monday, November 16, 2009, 11:11 AM
>
> the temperature plot should look like what you requested in your input.
> check the mdout file- does sander recognize your request for temperature
> change?
>
> note that a temp0 of 2000 will almost certainly give you problems unless
> you
> add additional restraints for things like chirality.
> this is a very high energy state and you can easily get cis-trans
> isomerizations and chirality inversions.
>
> On Sun, Nov 15, 2009 at 11:42 PM, Jio M <jiomm_at_yahoo.com> wrote:
>
> > Dear Sir,
> >
> >
> >
> > I am using following input file
> >
> > &cntrl
> >
> >
> > nstlim=1050000,
> >
> > ntt=3, gamma_ln=5,
> >
> >
> > scee=1.2,
> >
> >
> > ntpr=500, pencut=0.1,
> >
> >
> > nmropt=1,
> >
> >
> > vlimit=10,
> >
> >
> > ntb=0,dt = 0.0005,cut=999,ntwx=500
> >
> > /
> >
> > &wt type='TEMP0', istep1=0,istep2=140000,
> >
> > value1=300.0, value2=2000.0
> >
> > /
> >
> > &wt type='TEMP0', istep1=140001,istep2=200000,
> >
> > value1=2000.0, value2=2000.0
> >
> > /
> >
> > &wt type='TEMP0', istep1=200001,istep2=340000,
> >
> > value1=2000.0, value2=1000.0
> >
> > /
> >
> > &wt type='TEMP0', istep1=340001,istep2=480000,
> >
> > value1=1000.0, value2=2000.0
> >
> > /
> >
> > &wt type='TEMP0', istep1=480001,istep2=620000,
> >
> > value1=2000.0, value2=1000.0
> >
> > /
> >
> > &wt type='TEMP0', istep1=620001,istep2=760000,
> >
> > value1=1000.0, value2=2000.0
> >
> > /
> >
> > &wt type='TEMP0', istep1=760001,istep2=900000,
> >
> > value1=2000.0, value2=1000.0
> >
> > /
> >
> > &wt type='TEMP0', istep1=900001,istep2=1050000,
> >
> > value1=1000.0, value2=300.0
> >
> > /
> >
> > &wt type='END'
> >
> > /
> >
> >
> >
> >
> >
> > --- On Sun, 11/15/09, Carlos Simmerling <carlos.simmerling_at_gmail.com>
> > wrote:
> >
> > From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
> > Subject: Re: [AMBER] slope {no reply}
> > To: "AMBER Mailing List" <amber_at_ambermd.org>
> > Date: Sunday, November 15, 2009, 7:07 PM
> >
> > for (1) it all depends on how you set the thermostat temp0, which
> > thermostat and what coupling constant. no way to predict your data
> > without that.
> >
> > On 11/15/09, Jio M <jiomm_at_yahoo.com> wrote:
> > >
> > >
> > >
> > >
> > > Dear Amber users,
> > >
> > >
> > >
> > > 1) I am performing annealing and want to plot temp vs steps graph ..is
> > > it neccessary that temp vs steps plot should give
> > > linear rise or fall of graph of slope 45 degree or it should be linear
> > > what so ever slope may be ?
> > >
> > >
> > >
> > > 2) same query as before.. can we solubilize the system with single
> > molecule
> > > instead of box solvent
> > >
> > >
> > >
> > > please suggest
> > >
> > >
> > >
> > > thanks and regards;
> > >
> > > Jiomm
> > >
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER_at_ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER_at_ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> > --
> > ===================================================================
> > Carlos L. Simmerling, Ph.D.
> > Professor, Department of Chemistry
> > CMM Bldg, Room G80 Phone: (631) 632-1336 Fax: 632-1555
> > Stony Brook University E-mail: carlos.simmerling_at_gmail.com
> > Stony Brook, NY 11794-5115 Web: http://www.simmerlinglab.org
> > ===================================================================
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber