AMBER Archive (2009)

Subject: Re: [AMBER] slope

From: Jio M (jiomm_at_yahoo.com)
Date: Mon Nov 16 2009 - 22:07:07 CST

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
> ===================================================================
>
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