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

ram bio rmbio861 at gmail.com
Mon Oct 26 11:38:25 CET 2009


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.

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
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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
>>>>>>> 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
>>>>> 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
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before
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>>> 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
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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