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 <jalem...@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 <jalem...@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 <jalem...@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 <jalem...@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
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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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--
========================================
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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Please search the archive at http://www.gromacs.org/search before
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or send it to gmx-users-requ...@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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--
========================================
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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--
========================================
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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