Hello,
Set ntwx to 1 and try to visualize what's happening to your system to make
it blow apart. Secondly, I would leave tol at its default value. Finally,
the restraints that you're applying appear to be applied to every atom in
the system, not just the backbone. To restrain the backbone, you can use
"restraintmask=".CA,N,C,O" and restraint_wt to set the strength of the
restraints. You'll have to get rid of the restraint cards at the bottom of
your input file, though. I would also leave vlimit at its default value.
Why are you changing it?
All the best,
Jason
On Mon, Jun 21, 2010 at 7:10 AM, Sangita Kachhap <sangita.imtech.res.in>wrote:
>
> Hello all
>
> I am doing constant pH simulation using Amber10.
> For this
> 1) I have minimize protein:
> a)using restraint on backbone with force constant 500.0
> b)whole sytem with restraint
>
> 2)Heating of system for 300ps with temperature increment 1K/1ps,during
> heating
> here i have used tol=.00001 though in manual for constant pH simulation
> it
> is tol=.000001. Actualy I have done it by mistake.Here I restraint backbone
> with
> foce constant 10.0 .
>
> Here is my input file:
> imin=0,
> irest=0,ntx=1,ntb=0,cut=30,
> ntpr=200,ntwx=200,ntwr=500,
> igb=2,ntc=2,ntf=2,nrespa=1,tautp=2.0,
> nstlim=150000,dt=.002,ntr=1,
> ntt=1,tempi=0,temp0=300,nmropt=1,
> scee=1.2,saltcon=0.1,tol=0.00001,vlimit=15,
> icnstph=1,solvph=4,ntcnstph=5
> &end
> &wt
> type='TEMP0', istep1=0, istep2=10000, value1=0, value2=20,
> &end
> &wt
> type='TEMP0', istep1=10001, istep2=20000, value1=20, value2=40,
> &end
> &wt ...........
>
> type='END'
> /
> Hold only backbone atom fixed
> 10.0
> FIND
> * * M *
> SEARCH
> RES 1 129
> END
> END
>
>
>
> 3)Equilibration for 300ps using restraint on backbone with force constant
> 1.0
> this time I use tol=.000001 then I got following error:
>
> vlimit exceeded for step 78066; vmax = 321.8661
> vlimit exceeded for step 78067; vmax = 24.5430
> vlimit exceeded for step 78082; vmax = 399.2392
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 5 2 19 21
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
>
> But when I chage it to tol=.00001 it run upto 300ps
>
>
> 4)In production run again I have use tol=.00001 it stop with following
> error :
>
> vlimit exceeded for step 262668; vmax = 111.4422
> vlimit exceeded for step 262669; vmax = 25.1137
> vlimit exceeded for step 262699; vmax = 1960.5580
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 2 2 19 21
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
>
>
> Here is the input file:
> imin=0,
> irest=1,ntx=7,ntb=0,cut=30,
> ntpr=200,ntwx=200,ntwr=500,
> igb=2,ntc=2,ntf=2,nrespa=1,tautp=2.0,
> nstlim=150000,dt=.002,
> ntt=1,tempi=300,temp0=300,
> scee=1.2,saltcon=0.1,tol=0.00001,vlimit=15,
> icnstph=1,solvph=4,ntcnstph=5
> /
>
>
> Where is the problem I am not getting so can anybody suggest me
>
> With regard
> Sangita Kachhap
> JRF
> BIC,IMTECH
> CHANDIGARH
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Jun 21 2010 - 07:30:16 PDT
