AMBER Archive (2004)

Subject: Re: AMBER: simulated anealing ...vlimit exceed

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Thu May 06 2004 - 06:47:48 CDT

you have VERY high initial vdw energy-
was the structure minimized first? can you run
any normal MD? it's good to try that before a
complicated input file.
carlos

----- Original Message -----
From: <anshul_at_imtech.res.in>
To: "amber mail reflector" <amber_at_scripps.edu>
Sent: Thursday, May 06, 2004 5:50 PM
Subject: AMBER: simulated anealing ...vlimit exceed

> hi all,
> I am trying to run simulated anealing on a protein but everytime i am
> getting the error of vlimit exceed. I am running it in vacuume conditions
> and according to the archive of mails i also reduced teh force constant
> for restraints to 2 ..but still the same thing. can anyone suggest
> something.
>
>
> input file:
>
> &ewald
> eedmeth=5,
> &end
> &cntrl
> imin=0, cut=30, nstlim=90000, ntt=1, ntx=1, irest=0,
> ntpr=500, ntwx=500, ntwe=500, tempi=10,
> ntb=0, ntr=1, dielc=4, vlimit=30,
> &end
> Input for restrained residues (A1-A166)
> 2
> RES 1 167
> END
> Input for restrained residues (A182-A276)
> 2
> RES 182 276
> END
> END
> &wt type='TEMP0', istep1=0,istep2=50000,value1=10.0,
> value2=500.0, &end
> &wt type='TEMP0', istep1=50001,istep2=60000,value1=500.0,
> value2=500.0, &end
> &wt type='TEMP0', istep1=60001,istep2=70000,value1=500.0,
> value2=300.0, &end
> &wt type='TEMP0', istep1=70001,istep2=90000,value1=300.0,
> value2=300.0, &end
> &wt type='TAUTP', istep1=0,istep2=60000,value1=0.5,
> value2=0.5 &end
> &wt type='TAUTP', istep1=60001,istep2=65000,value1=2.0,
> value2=2.0 &end
> &wt type='TAUTP', istep1=65001,istep2=70000,value1=0.2,
> value2=0.2 &end
> &wt type='TAUTP', istep1=70001,istep2=90000,value1=0.5,
> value2=0.5 &end
> &wt type='END' &end
>
> output::
>
> RESULTS
> --------------------------------------------------------------------------
------
>
> ---------------------------------------------------
>
> eedmeth=4: Setting switch to one everywhere
>
> ---------------------------------------------------
> | Local SIZE OF NONBOND LIST = 4988756
> | TOTAL SIZE OF NONBOND LIST = 4988756
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 9.88 PRESS = 0.0
> Etot = ************ EKtot = 129.0390 EPtot = ************
> BOND = 772.3704 ANGLE = 1001.8422 DIHED = 2404.3438
> 1-4 NB = 1253.7810 1-4 EEL = 2187.4793 VDWAALS = ************
> EELEC = -4664.7256 EHBOND = 0.0000 RESTRAINT = 0.0000
>
> -------------------------------------------------------------------------- 

----
>
>  vlimit exceeded for step  0; vmax =   2.16726961E+12
>  vlimit exceeded for step  1; vmax =   1.25533206E+12
>  vlimit exceeded for step  2; vmax =   53538856.1
>  vlimit exceeded for step  3; vmax =   445647.94
>  vlimit exceeded for step  4; vmax =   1058268.05
>  vlimit exceeded for step  5; vmax =   2.00528168E+11
>  vlimit exceeded for step  6; vmax =   767387.095
>  vlimit exceeded for step  7; vmax =   322935852.
>  vlimit exceeded for step  8; vmax =   17379772.
>  vlimit exceeded for step  9; vmax =   4566640.04
>
>
>            With regards
> Anshul
>
>
>
>
>
>
>
>
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