AMBER Archive (2004)

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

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Thu May 06 2004 - 08:24:02 CDT

did you use exactly the same input file for
MD and minimization, except the imin value?
did you change anything else, like eedmeth, or use_pme?
are you sure you are using the minimized coordinate
as input to sander for MD? compare the energies
from the last step of minimization to the first energy
from the MD run.
carlos

----- Original Message -----
From: <anshul_at_imtech.res.in>
To: <amber_at_scripps.edu>
Sent: Thursday, May 06, 2004 7:14 PM
Subject: Re: AMBER: simulated anealing ...vlimit exceed

>
> 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
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> >
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