Hi,
Your minimization protocol (2 phases of NTV MD for a total of 20 ps)
is probably not adequate. Systems with explicit solvent in particular
require very careful minimization. You will most certainly want to run
a minimization (imin=1) before anything else, followed by a series of
short NTV MD sims, keeping the solute fixed with weak restraints,
gradually relaxing them. This will allow the solvent to relax. After
this you'll want to run another minimization followed by a series of
short NTP MD sims, again keeping the solute fixed with restraints,
gradually relaxing them. This will allow the density of the system to
equilibrate. With restraints, generally I run several MD simulations
where I start off restraining all heavy atoms, then all backbone
atoms, then I remove the restraints entirely. Once you see your system
density reaching a stable value your system should be in a reasonable
place for further simulation.
If you haven't already I recommend you check out Amber Tutorial B1
(
http://ambermd.org/tutorials/basic/tutorial1/), particularly section
5, which has to do with minimization/equilibration in explicit
solvent. Hope this is helpful, good luck!
-Dan
On Fri, Sep 23, 2011 at 4:05 AM, Aparna P <aparnaspap.gmail.com> wrote:
> Thanks a lot 4 your reply sir.
> I have seen some distortions when i viewed it in VMD.
>
> This is my minimisation input, *min1.in*.
>
> 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 YDNA fixed with weak
> restraints
> 10.0
>
> RES 1
> 20
> END
>
> END
>
>
> *min2.in*
>
> DNA : 10ps MD with res 10 kcal at const
> volume
> &cntrl
>
> imin =
> 0,
> irest =
> 1,
> ntx =
> 5,
> ntb =
> 1,
> cut =
> 10,
> ntr =
> 1,
> ntc =
> 2,
> ntf =
> 2,
> tempi =
> 145.83,
> temp0 =
> 300.0,
> ntt =
> 3,
> gamma_ln =
> 1,
> nstlim = 50000, dt =
> 0.001,
> ntpr = 500, ntwx = 500, ntwr =
> 1000,
> nmropt =
> 1,
> /
>
> &wt
>
> type = 'TEMP0', istep1 = 1, istep2 =25000, value1 = 145.83, value2 =
> 300.0,
> /
>
> &wt
>
>
> type='END'
>
> /
>
>
>
> Group Input for restrained
> atoms
> 10.0
>
> RES 1
> 20
> END
>
> END
>
>
>
> I have done these minimisations only.
>
> The problem of vlimit arises from the first production run output itself.and
> with that error the program continues running and the error increases
> gradually and get stopped.
> >From first MD output itself the error starts.
> here is the error
>
> 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 = 18000 TIME(PS) = 18.000 TEMP(K) = 102.65 PRESS =
> 0.0
> Etot = -49248.1272 EKtot = 2609.1759 EPtot =
> -51857.3032
> BOND = 98.5736 ANGLE = 622.0273 DIHED =
> 568.0625
> 1-4 NB = 265.7208 1-4 EEL = -5598.8238 VDWAALS =
> 7905.8834
> EELEC = -55768.2035 EHBOND = 0.0000 RESTRAINT =
> 49.4566
> EAMBER (non-restraint) = -51906.7598
> Ewald error estimate: 0.6970E-05
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
> ===============================================================================
> vlimit exceeded for step 18001; vmax = 21.0253
> vlimit exceeded for step 18007; vmax = 20.6049
> vlimit exceeded for step 18011; vmax = 22.0151
> vlimit exceeded for step 18012; vmax = 20.7999
> vlimit exceeded for step 18046; vmax = 22.3654
> vlimit exceeded for step 18047; vmax = 20.6767
> vlimit exceeded for step 18050; vmax = 20.0744
> vlimit exceeded for step 18087; vmax = 20.3247
> vlimit exceeded for step 18096; vmax = 20.1899
>
> NSTEP = 7000 TIME(PS) = 57.000 TEMP(K) = 181.67 PRESS =
> 0.0
> Etot = -45896.5439 EKtot = 4617.8243 EPtot =
> -50514.3682
> BOND = 123.4178 ANGLE = 673.3129 DIHED =
> 578.1077
> 1-4 NB = 259.3839 1-4 EEL = -5552.7593 VDWAALS =
> 7541.6715
> EELEC = -54229.7822 EHBOND = 0.0000 RESTRAINT =
> 92.2794
> EAMBER (non-restraint) = -50606.6476
> Ewald error estimate: 0.2620E-03
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
> ===============================================================================
> vlimit exceeded for step 7382; vmax = 21.0734
> vlimit exceeded for step 7383; vmax = 27.3836
> vlimit exceeded for step 7384; vmax = 20.5762
> vlimit exceeded for step 7386; vmax = 20.3252
> vlimit exceeded for step 7387; vmax = 21.3863
> vlimit exceeded for step 7390; vmax = 20.3066
> vlimit exceeded for step 7394; vmax = 20.9089
> vlimit exceeded for step 7409; vmax = 20.8912
>
> likewise the error increases from ps to ps and at last it got stopped at
> 3374ps.
> what can I do?
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Received on Fri Sep 23 2011 - 05:00:03 PDT
