AMBER Archive (2005)Subject: Re: AMBER: question about TGMD: vlimit exceeded for step
From: xhu1_at_memphis.edu
Date: Fri Apr 08 2005  16:55:05 CDT
Thank you very much, Vikror. But I am confused. Maybe I didn't make
myself clear in my last email: the overall RMSD(residue 3122) between
the initial structure and the reference structure is 4.345, so I set
tgtrmsd=4.435. now I want to apply targeted MD at residue 8186, all
the other is free to move, then see if the simulated structure
achieves the reference structure or not at the end. By this,I can
judge if the residues 8186 play as a key in this sturcuture change.
after reading your reply, besides switching the maskes, I also need to
change the tgtrmsd value. this value should be the RMSD of residue 81
86 between the initail and the reference structure, am I right? Thanks
again
Shawn
 Original Message 
From: Viktor Hornak <hornak_at_csb.sunysb.edu>
Date: Friday, April 8, 2005 3:47 pm
Subject: Re: AMBER: question about TGMD: vlimit exceeded for step
>
> I think your masks are reversed. According to your input you
> overlap
> your molecule to a reference by residues 8186 and calculate the
> force
> based on RMSD of residues 3122. You should try to switch the
> masks,
> such as: tgtfitmask=':3122', tgtrmsmask=':8186 & !@H=', or use
> positional restraints (ntr=1) for atoms :380,87122
> (restraintmask=':380,87122', restraint_wt = 2.0, or such) and
> use
> targeted md for :8186 (tgtrmsmask=':8186')...
>
> Cheers,
> Viktor
>
> xhu1_at_memphis.edu wrote:
>
> >Dear all,
> >
> >I am trying to run TGMD for a system: a 124residue protein in a
> >waterbox.
> >
> >Using AMBER7, weighted TGTRMSD from 4.345 to 0, TGTMDMDFRC=10 or
> 5 or
> >1, restrain force applied on residue 3122, job running OK. then
> I
> >tried to apply the restraint force on residue 8186 only, to see
> if
> >the structure will go to the reference structure as well. AMBER7
> seems
> >not be able to do this. I move to AMBER8. Here is the input file:
> >*****************************************************************
> >#Data collection at 298K
> > &cntrl
> > IMIN = 0,ntx=5,irest=1,
> > ntpr=10, ntwr=500,
> > ntb=1,ntr=0,
> > ntf=2,ntc=2,
> > cut=8.5, nscm = 1000,
> > NSTLIM = 400000, DT = 0.002,
> > NTWX=500, NTWV=500,NTWE=500,
> > TEMP0 = 298.0, TEMPI=298.0, NTT=1, TAUTP=2.0,
> > nmropt=1, itgtmd=1, tgtrmsd=4.345, tgtmdfrc=10.00,
> > tgtrmsmask=":3122", tgtfitmask=":8186 & !@H=",
> > &end
> > &wt
> > TYPE='TGTRMSD', istep1 =0, istep2 = 200000,
> > value1 = 4.345, value2 = 0.3,
> > &end
> > &wt
> > TYPE='TGTRMSD', istep1 =200001, istep2 = 400000,
> > value1 = 0.3, value2 = 0.,
> > &end
> > &wt
> > type="END",
> > &end
> > &rst
> > iat(1)=0,
> > &end
> >END
>
>**********************************************************************
*
> >
> >I got a problem: job stopped immediately, and gave the informatin
> as
> >following:
> >
> >*********************************************
> >
> > NSTEP = 10 TIME(PS) = 360.020 TEMP(K) = 5403.88
> PRESS
> >= 0.0
> > Etot = 867849.0298 EKtot = 181470.7791 EPtot =
>
> >686378.2507
> > BOND = 1342.9958 ANGLE = 1534.9087 DIHED =
>
> >1235.1722
> > 14 NB = 1138.3272 14 EEL = 5449.3066 VDWAALS =
>
> >9292.6310
> > EELEC = 64101.8524 EHBOND = 0.0000 RESTRAINT =
>
> >730486.7616
> > EAMBER (nonrestraint) = 44108.5108
> > Ewald error estimate: 0.2247E04
> >Current RMSD from reference: 13.246
> >Current target RMSD: 4.345
> > 
> 
> >
> > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion =
>
> >0.000
>
>======================================================================
=
> > vlimit exceeded for step 11 ; vmax = 21.4771801052079
> > vlimit exceeded for step 12 ; vmax = 1952.41027295489
> >
> > Coordinate resetting (SHAKE) cannot be accomplished,
> > deviation is too large
> > NITER, NIT, LL, I and J are : 0 2 439 882 883
> >
> > Note: This is usually a symptom of some deeper
> > problem with the energetics of the system.
>
>**********************************************************************
*
> >
> >I noticed that the "Current RMSD from reference" is huge
> different
> >from the "Current target RMSD". Is my TGTMDFRC too large?? I
> decreased
> >this value to 5, then 1, after running several tens steps, jobs
> >stopped for the same reason too. I read some emails in the
> mailing
> >list. the value of TGTMDFRC between 15 or 110 should be OK.
> then
> >does my input file have a problem?
> >
> >Thank you very much for your help!
> >
> >Shawn
> >
> >

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