AMBER Archive (2004)

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

From: anshul_at_imtech.res.in
Date: Thu May 06 2004 - 18:14:53 CDT

Dear Carlos

The system was minimized before performing simulated annealing. I
minimized it till the change in the energy change was stable and vdw
energy was also negative.
I also tried to run normal MD but with same results.

Can u suggest any changes that can overcome this problem.
I also tried to check the overlapps in the structure using checkoverlap
command of ptraj but it was not able to open the file in r mode.
can u tell me what this means??

With regards
Anshul

On Thu, 6 May 2004, Carlos Simmerling wrote:

> 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
> >
> >
> >
> >
> >
> >
> >
> >
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu