[gmx-users] Error during NVT equillibration with nvt.log file

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 26 11:58:26 CET 2009



ram bio wrote:
> Dear Justin,
> 
> As per the suggestions, I have run NPT equillibration (without
> constraints) for 1ns and observed the average values and plots in the
> xmgrace as follows:
> 
> 1) Pressure
> 
> Energy                      Average       RMSD     Fluct.      Drift  Tot-Drift
> -------------------------------------------------------------------------------
> Pressure (bar)             0.967068    315.557    315.557 -0.00139934   -1.39934
> 
> In the pressure.xvg plot the pressure was the same through out the
> equilibration, that is no rise or fall in the graph, fluctuating in
> the same range.
> 
> 2) Density
> 
> Energy                      Average       RMSD     Fluct.      Drift  Tot-Drift
> -------------------------------------------------------------------------------
> Density (SI)                1010.05    6.13912    4.17568  0.0155894    15.5894
> 
> In the density.xvg plot the density in the beginning was around 984
> and then increased upto 500 ps then onwards was the same through out
> the equilibration, that is no rise or fall in the graph, fluctuating
> in the same range.
> 
> 3) temperature
> 
> Energy                      Average       RMSD     Fluct.      Drift  Tot-Drift
> -------------------------------------------------------------------------------
> Temperature                     323    1.68979    1.68965 7.75704e-05  0.0775705
> Heat Capacity Cv:      12.4723 J/mol K (factor = 2.73692e-05)
> 
> In the temperature.xvg plot the pressure was the same through out the
> equilibration, that is no rise or fall in the graph, fluctuating in
> the same range.
> 
> 4) Box-x
> 
> Statistics over 1000001 steps [ 0.0000 thru 1000.0001 ps ], 1 data sets
> All averages are exact over 1000001 steps
> 
> Energy                      Average       RMSD     Fluct.      Drift  Tot-Drift
> -------------------------------------------------------------------------------
> Box-X                       6.81637 0.00919707 0.00692067 -2.09829e-05
> -0.0209829
> 
> In the box-x.xvg plot the value decreased from 6.82 - 6.84 to 6.79 -
> 6.81 after the 500 ps and then was the same through out the
> equilibration, that is no rise or fall in the graph, fluctuating in
> the same range.
> 
> 5) Box-Y  the trend was same as  X dimension
> 
> Energy                      Average       RMSD     Fluct.      Drift  Tot-Drift
> -------------------------------------------------------------------------------
> Box-Y                       6.84395 0.00923428 0.00694867 -2.10678e-05
> -0.0210678
> 
> 
> 5) Box-Z  the trend was same as  X dimension
> 
> Statistics over 1000001 steps [ 0.0000 thru 1000.0001 ps ], 1 data sets
> All averages are exact over 1000001 steps
> 
> Energy                      Average       RMSD     Fluct.      Drift  Tot-Drift
> -------------------------------------------------------------------------------
> Box-Z                        9.0932  0.0438719   0.036307 -8.53145e-05
> -0.0853146
> 
> In the box-z.xvg plot the value started from 9.3 and decreased to 9.03
> at the 500 ps and then the values were fluctuating around this value
> in the same run.
> 
> Please suggest me are my equilibrated  parameters ok for the MD
> production run or i have to look for some more parameters and is it ok
> if i run the production phase also without constraints  and position
> restraints.
> 

You've presented six pieces of data that have all stabilized.  You have to make 
the decision as to whether or not your equilibration is sufficient; you can't 
rely on others who know nothing about your project or its goals to continually 
check it and tell you if it's right.

-Justin

> The mdp file used for NPT is as  below:
> 
> title		= NPT Equilibration
> define		= -DPOSRES	
> integrator	= md		
> nsteps		= 1000000	
> dt		= 0.001		
> nstxout		= 100		
> nstvout		= 100		
> nstenergy	= 100		
> nstlog		= 100		
> continuation	= yes		
> constraint_algorithm = lincs	
> constraints	= none  	
> lincs_iter	= 1		
> lincs_order	= 4		
> ns_type		= grid		
> nstlist		= 5		
> rlist		= 1.2		
> rcoulomb	= 1.2		
> rvdw		= 1.2		
> coulombtype	= PME		
> pme_order	= 4		
> fourierspacing	= 0.16		
> tcoupl		= Nose-Hoover		
> tc-grps		= Protein DPPC	SOL_CL-	
> tau_t		= 0.1	0.1	0.1	
> ref_t		= 323 	323	323	
> pcoupl		= Parrinello-Rahman	
> pcoupltype	= semiisotropic		
> tau_p		= 5.0			
> ref_p		= 1.0	1.0		
> compressibility = 4.5e-5	4.5e-5	
> pbc		= xyz		
> DispCorr	= EnerPres	
> gen_vel		= no		
> nstcomm         = 1
> comm-mode       = Linear
> comm-grps       = Protein_DPPC SOL_CL-
> 
> 
> Thanks,
> 
> Ram
> 
> On Tue, Oct 20, 2009 at 7:59 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>> ram bio wrote:
>>> Dear Justion,
>>>
>>> When I executed the command g_energy -f anneal_npt1.edr, the output
>>> for temperature and pressure were as under:
>>>
>>> Statistics over 500001 steps [ 0.0000 thru 500.0000 ps ], 1 data sets
>>> All averages are exact over 500001 steps
>>>
>>> Energy                      Average       RMSD     Fluct.      Drift
>>>  Tot-Drift
>>>
>>> -------------------------------------------------------------------------------
>>> Temperature                  161.41    93.1199          0   0.645591
>>>  322.796
>>> Heat Capacity Cv:       24.906 J/mol K (factor = 0.332832)
>>>
>>> Statistics over 500001 steps [ 0.0000 thru 500.0000 ps ], 1 data sets
>>> All averages are exact over 500001 steps
>>>
>>> Energy                      Average       RMSD     Fluct.      Drift
>>>  Tot-Drift
>>>
>>> -------------------------------------------------------------------------------
>>> Pressure (bar)             -7.96937    115.169    114.406  0.0916656
>>>  45.8329
>>>
>>> i am unable to understand from these parameters, whether the system is
>>> ok for future steps.
>> Because simply looking at averages is less useful than looking at the plots.
>>  I asked whether the temperature had stabilized, not what it's average value
>> was. Consider this - you're constantly increasing the temperature, so an
>> average is useless.  Look at the plot that g_energy gives you and make sure
>> the increase is as you would expect.  Probably a further NPT equilibration
>> is needed to make sure that the temperature will remain stable without the
>> influence of annealing.
>>
>> Same thing for pressure - look at the plot.  Wide fluctuations will occur,
>> so that's not a problem.  The trend is what is important (i.e., running
>> average in xmgrace).  Is the pressure leveling off?  The average is more
>> meaningful here, and it looks a bit low, but as I advise in my tutorial,
>> equilibrating membrane systems takes a *long* time, anyway.
>>
>> -Justin
>>
>>> Regarding the gaps in the lipid bilayers,now when i visualized the
>>> .trr file in the VMD there were no gaps in the lipid bilayer, that is
>>> they did not move apart.
>>>
>>> Please help.
>>>
>>> Thanks
>>>
>>> Ram
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Tue, Oct 20, 2009 at 7:40 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>>> ram bio wrote:
>>>>
>>>> <snip>
>>>>
>>>>> Now as i would like to proceed further, please suggest me how to
>>>>> confirm that the simulated annealing was proper and also please let me
>>>>> know can i now go to npt equillibration using the output of simulated
>>>>> annealing as input to npt equilibration.
>>>>>
>>>> Like you would anything else.  Have the temperature and pressure
>>>> stabilized?
>>>>  Is your structure reasonable (no gaps, etc)?
>>>>
>>>> -Justin
>>>>
>>>>> Like I am going to use the following command to run the npt
>>>>> equillibration:
>>>>>
>>>>> grompp -f npt.mdp -c anneal_npt1.gro -t anneal_npt.trr -p topol.top -n
>>>>> index.ndx -o npt.tpr
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Ram
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Fri, Oct 16, 2009 at 10:14 PM, Justin A. Lemkul <jalemkul at vt.edu>
>>>>> wrote:
>>>>>> ram bio wrote:
>>>>>>> Dear Justin,
>>>>>>>
>>>>>>> Thanks and I tried your suggestion, that is minimizing the system
>>>>>>> without restraints and increasing the Fmax to 1000, the mdp file used
>>>>>>> is as follows:
>>>>>>>
>>>>>> Note that I only suggested EM, not necessarily Fmax < 1000.  You
>>>>>> original
>>>>>> post contained an even lower Fmax, suggesting that you can do better
>>>>>> than
>>>>>> 1000.  The parameters in my tutorial are somewhat generic; you should
>>>>>> alter
>>>>>> them to suit your needs.
>>>>>>
>>>>>> <snip>
>>>>>>
>>>>>> Please note that the headers of log files are typically unnecessary
>>>>>> when
>>>>>> posting the .mdp file.
>>>>>>
>>>>>>> please suggest me is it ok to remove the constraints and run the NVT
>>>>>>> equillibration.
>>>>>>>
>>>>>> You can try it, but I doubt it will make a difference.  Your simulation
>>>>>> is
>>>>>> crashing before it is even starting, making it very difficult to
>>>>>> diagnose.
>>>>>>  You probably need to re-build the system, using as rigorous criteria
>>>>>> as
>>>>>> possible during the InflateGRO steps to ensure that you don't have any
>>>>>> improper atomic overlap.  In my experience, if the simulation is
>>>>>> failing
>>>>>> at
>>>>>> step 0, there is no hope for coaxing the system into working.  The
>>>>>> configuration simply isn't reasonable.
>>>>>>
>>>>>> -Justin
>>>>>>
>>>>>>> Thanks
>>>>>>>
>>>>>>> Ram
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Fri, Oct 16, 2009 at 9:27 PM, Justin A. Lemkul <jalemkul at vt.edu>
>>>>>>> wrote:
>>>>>>>> ram bio wrote:
>>>>>>>>> Dear Gromacs users,
>>>>>>>>>
>>>>>>>>> I am doing protein in lipid-bilayer simulation and i am following
>>>>>>>>> the
>>>>>>>>> procedure as per justin tutorial. I am able to insert the protein in
>>>>>>>>> lipid bilayer and minimize the system as per Inflategro
>>>>>>>>> procedure,during the total procedure the system was minimized in
>>>>>>>>> every
>>>>>>>>> step.Then, I solvated and ionized sytem and minimized using the
>>>>>>>>> following mdp file:
>>>>>>>>>
>>>>>>>>> ; minim.mdp - used as input into grompp to generate em.tpr
>>>>>>>>> ; Parameters describing what to do, when to stop and what to save
>>>>>>>>> define = -DSTRONG_POSRES
>>>>>>>>> integrator      = steep         ; Algorithm (steep = steepest
>>>>>>>>> descent
>>>>>>>>> minimization)
>>>>>>>>> emtol           = 500.0         ; Stop minimization when the maximum
>>>>>>>>> force < 1000.0 kJ/mol/nm
>>>>>>>>> emstep          = 0.01          ; Energy step size
>>>>>>>>> nsteps          = 50000         ; Maximum number of (minimization)
>>>>>>>>> steps to perform
>>>>>>>>>
>>>>>>>>> ; Parameters describing how to find the neighbors of each atom and
>>>>>>>>> how
>>>>>>>>> to calculate the interactions
>>>>>>>>> nstlist         = 1             ; Frequency to update the neighbor
>>>>>>>>> list and long range forces
>>>>>>>>> ns_type         = grid          ; Method to determine neighbor list
>>>>>>>>> (simple, grid)
>>>>>>>>> rlist           = 1.2           ; Cut-off for making neighbor list
>>>>>>>>> (short range forces)
>>>>>>>>> coulombtype     = PME           ; Treatment of long range
>>>>>>>>> electrostatic interactions
>>>>>>>>> rcoulomb        = 1.2           ; Short-range electrostatic cut-off
>>>>>>>>> rvdw            = 1.2           ; Short-range Van der Waals cut-off
>>>>>>>>> pbc             = xyz           ; Periodic Boundary Conditions
>>>>>>>>> (yes/no)
>>>>>>>>>
>>>>>>>>> the output was as follows:
>>>>>>>>>
>>>>>>>>> Steepest Descents converged to Fmax < 500 in 4770 steps
>>>>>>>>> Potential Energy  = -3.8820288e+05
>>>>>>>>> Maximum force     =  4.4803549e+02 on atom 3573
>>>>>>>>> Norm of force     =  1.7854408e+01
>>>>>>>>>
>>>>>>>>> As the potential energy and Fmax values were agreeable , I proceeded
>>>>>>>>> to equillibrate the system using NVT.
>>>>>>>>>
>>>>>>>> Did you minimize the structure without restraints, prior to NVT?
>>>>>>>>
>>>>>>>> <snip>
>>>>>>>>
>>>>>>>>>       Angle       G96Angle    Proper Dih. Ryckaert-Bell.  Improper
>>>>>>>>> Dih.
>>>>>>>>>  2.20077e+04    8.54042e+03    6.78950e+03    4.34650e+03
>>>>>>>>>  3.03266e+03
>>>>>>>>>       LJ-14     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb
>>>>>>>>> (SR)
>>>>>>>>>  4.76527e+03    5.50236e+04    8.36617e+06   -2.20019e+03
>>>>>>>>> -4.46844e+05
>>>>>>>>>  Coul. recip. Position Rest.      Potential    Kinetic En.   Total
>>>>>>>>> Energy
>>>>>>>>>  -1.65524e+05    1.07769e+01    7.85612e+06    5.88813e+10
>>>>>>>>>  5.88892e+10
>>>>>>>>>  Conserved En.    Temperature Pressure (bar)  Cons. rmsd ()
>>>>>>>>>  5.88892e+10    2.23805e+08    1.21713e+09    3.10245e+01
>>>>>>>>>
>>>>>>>> In my experience, the combination of an astronomically high
>>>>>>>> temperature
>>>>>>>> and
>>>>>>>> a repulsive temperature is indicative of restraining an
>>>>>>>> unrestrainable
>>>>>>>> starting structure.  Try the EM I suggested above.  Other than that,
>>>>>>>> as
>>>>>>>> I've
>>>>>>>> suggested before, see the Advanced Troubleshooting page I created in
>>>>>>>> the
>>>>>>>> tutorial.
>>>>>>>>
>>>>>>>> -Justin
>>>>>>>>
>>>>>>>>> Please help me to proceed further and let me know where are the
>>>>>>>>> mistakes lying and how to overcome them.
>>>>>>>>>
>>>>>>>>> Thanks in advance,
>>>>>>>>>
>>>>>>>>> Ram
>>>>>>>>> _______________________________________________
>>>>>>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>>>>> Please search the archive at http://www.gromacs.org/search before
>>>>>>>>> posting!
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>>>>>>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>>>>>>
>>>>>>>> --
>>>>>>>> ========================================
>>>>>>>>
>>>>>>>> Justin A. Lemkul
>>>>>>>> Ph.D. Candidate
>>>>>>>> ICTAS Doctoral Scholar
>>>>>>>> Department of Biochemistry
>>>>>>>> Virginia Tech
>>>>>>>> Blacksburg, VA
>>>>>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>>>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>>>>>
>>>>>>>> ========================================
>>>>>>>> _______________________________________________
>>>>>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>>>> Please search the archive at http://www.gromacs.org/search before
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>>>>>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>>>>>
>>>>>> --
>>>>>> ========================================
>>>>>>
>>>>>> Justin A. Lemkul
>>>>>> Ph.D. Candidate
>>>>>> ICTAS Doctoral Scholar
>>>>>> Department of Biochemistry
>>>>>> Virginia Tech
>>>>>> Blacksburg, VA
>>>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>>>
>>>>>> ========================================
>>>>>> _______________________________________________
>>>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>> Please search the archive at http://www.gromacs.org/search before
>>>>>> posting!
>>>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>>>> interface
>>>>>> or send it to gmx-users-request at gromacs.org.
>>>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>>>
>>>> --
>>>> ========================================
>>>>
>>>> Justin A. Lemkul
>>>> Ph.D. Candidate
>>>> ICTAS Doctoral Scholar
>>>> Department of Biochemistry
>>>> Virginia Tech
>>>> Blacksburg, VA
>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>
>>>> ========================================
>>>> _______________________________________________
>>>> gmx-users mailing list    gmx-users at gromacs.org
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>>>> Please search the archive at http://www.gromacs.org/search before
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>>>> or send it to gmx-users-request at gromacs.org.
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>>>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
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>>
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================



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