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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