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
