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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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
========================================
_______________________________________________
gmx-users mailing list gmx-users@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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or send it to gmx-users-requ...@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
========================================
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