AMBER Archive (2004)

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

From: Venkata S Koppuravuri (kvsuneel_at_linus.bmb.wright.edu)
Date: Mon May 17 2004 - 12:00:44 CDT

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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