Hi,
Vlimit/SHAKE errors often indicate the system has not been adequately
minimized. What procedure did you use to minimize/equilibrate prior to
running MD? The SHAKE error message indicates that the problem is
between atoms 21 and 22 (the last two numbers in the NITER line). Have
you tried visualizing this part of the structure to see if everything
looks OK?
-Dan
On Thu, Sep 22, 2011 at 4:00 AM, Aparna P <aparnaspap.gmail.com> wrote:
> Hi
>
> I am working on Biomolecular modelling.i have build a model of a biomolecule
> and now i am doing MD of that.
> I have run the minimisation
> My input is
>
> DNA 10ps MD with res 10 kcal/mol restraints
>
> &cntrl
>
> imin =
> 0,
> irest =
> 0,
> ntx =
> 1,
> ntb =
> 1,
> cut =
> 10,
> ntr =
> 1,
> ntc =
> 2,
> ntf =
> 2,
> tempi =
> 0.0,
> temp0 =
> 150.0,
> ntt =
> 3,
> gamma_ln =
> 1,
> nstlim = 50000, dt =
> 0.001,
> ntpr = 500, ntwx = 500, ntwr =
> 1000,
> nmropt =
> 1,
> /
>
> &wt type = 'TEMP0', istep1 = 0, istep2 = 25000, value1 = 0.0, value2 =
> 150.0,
> /
>
> &wt type =
> 'END'
> /
>
> Keep DNA fixed with weak
> restraints
> 10.0
>
> RES 1
> 20
> END
>
> END
>
> But it shows Vlimit exeeding problem aftr some ps.as follows
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
> 0.0
> Etot = -60915.8860 EKtot = 0.0000 EPtot =
> -60915.8860
> BOND = 46.0249 ANGLE = 545.6061 DIHED =
> 535.0389
> 1-4 NB = 259.1070 1-4 EEL = -5583.3665 VDWAALS =
> 10203.6931
> EELEC = -66921.9894 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> Ewald error estimate: 0.2769E-03
>
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>
>
> NSTEP = 10000 TIME(PS) = 20.000 TEMP(K) = 58.22 PRESS =
> 0.0
> Etot = -51315.5240 EKtot = 1479.8931 EPtot =
> -52795.4171
> BOND = 75.7294 ANGLE = 599.8928 DIHED =
> 552.7123
> 1-4 NB = 272.6463 1-4 EEL = -5596.9545 VDWAALS =
> 8170.3153
> EELEC = -56901.3723 EHBOND = 0.0000 RESTRAINT =
> 31.6135
> EAMBER (non-restraint) = -52827.0306
> Ewald error estimate: 0.8510E-04
> -----------------------------------------------------------------------
>
> =======
> vlimit exceeded for step 10315; vmax = 256.3785
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 0 4 21 22
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
>
> I have used 1fs instad of 2 fs.then there was difference.But still it shows
> vlimit exeeding problem and now the programme got stopped itself.
> I have tried different input values.But I cannot tackle the problem.Is that
> because the structure is made by model building.?
> I have used the inprd structure as the reference structure.
>
> Kindly give me a suggestion.
>
> regrds
> Aparna.P
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Received on Thu Sep 22 2011 - 05:00:03 PDT
