AMBER Archive (2004)

Subject: Re: AMBER: Simulated annealing ...vlimit problem

From: Narang Manpreet Kaur (preetdbs_at_iitr.ernet.in)
Date: Tue May 18 2004 - 09:09:31 CDT

 Hi Venkata,
Can u please send me the input file for your simmulated annealing
protocol ( how u r raising the temperature etc) i tried long bak but
temperature showed lot of fluctuations and was never maintained according
to he protocol. i shall be highly obliged.
Thanking you,
Manpreet Kaur Narang
        

*******************************************************************************
Manpreet Kaur Narang
C/o Dr. Ritu Barthwal
Research Scholar
Structure Biology & Biophysics Lab
Lab No. G1 & G-4
Deptt.Biotechnology
Indian Institute of Technology Roorkee (IITR)
Roorkee, 247 667 India
******************************************************************************
Email:- preetdbs_at_iitr.ernet.in, preetdbs_at_indiatimes.com

On Mon, 17 May 2004, Venkata S Koppuravuri wrote:

>
> Hi All,
>
> I am trying to do a Simulated annealing on a protein structure and I got
> the following error.
> --------------------------
> vlimit exceeded for step 0 ; vmax = 25661.90229977621
> vlimit exceeded for step 1 ; vmax = 271.9070745233018
> vlimit exceeded for step 2 ; vmax = 11.03999138171793
> vlimit exceeded for step 3 ; vmax = 6.104038534855053
> vlimit exceeded for step 4 ; vmax = 6.405817372735854
> ....
> ....
> --------------------------
>
> I have protonated the structure but have not hydrated it. Below is the
> script that i have used.
>
> -------------
> &cntrl
> nstlim=20000, pencut=-0.001, nmropt=1,
> ntpr=200, ntt=1, ntwx=200,
> cut=15.0, ntb=0, vlimit=5,
> lastist = 7500000, lastrst = 7500000,
> /
> &ewald
> eedmeth=5,
> /
> #
> #Simple simulated annealing algorithm:
> #
> #from steps 0 to 5000: heat the system to 600K
> #from steps 5001-18000:re-cool to low temperatures with long tautp
> #from steps 18001-20000: final cooling with short tautp
> #
> &wt type='TEMP0', istep1=0,istep2=5000,value1=600.,
> value2=600., /
> &wt type='TEMP0', istep1=5001, istep2=18000, value1=600.0,
> value2=100.0, /
> &wt type='TEMP0', istep1=18001, istep2=20000, value1=0.0,
> value2=0.0, /
>
> &wt type='TAUTP', istep1=0,istep2=5000,value1=0.4,
> value2=0.4, /
> &wt type='TAUTP', istep1=5001,istep2=18000,value1=4.0,
> value2=4.0, /
> &wt type='TAUTP', istep1=18001,istep2=19000,value1=1.0,
> value2=1.0, /
> &wt type='TAUTP', istep1=19001,istep2=20000,value1=0.1,
> value2=0.05, /
>
> &wt type='END' /
>
> -------------
>
> I have also done the normal MD on the same structure which went fine, but
> in this case I have protonated it and also hydrated it.
>
> Can someone please help me solve the problem.
>
> Thanks in advance
>
> -Venkat
>
> On Sat, 15 May 2004, David A. Case wrote:
>
> > On Fri, May 14, 2004, Venkata S Koppuravuri wrote:
> >
> > I am trying to do Simulated annealing on a protein structure and got the
> > vlimit error.
> >
> > We would need a lot more information to be of any help here.
> >
> > ...regards...dac
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