hema dhevi wrote:
hai justin,
ya i am working on actual KALP tutorial only
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html
and i am using the pdb file which is given in the website. This is
the first time i am doing MD simulation
for transmembrane proteins before using the protein of my interest i
tried it with the peptide given the tutorial.
hereby i am attaching the .mdp file which i am using
; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent
minimization)
emtol = 1000.0 ; 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 ho
w 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)
Well, the KALP system is very robust (hence why I wrote the tutorial), so the
problem is likely coming from your machine. Do you have any other computer you
can try it on? Otherwise, post the commands you used to install Gromacs (any
special configuration flags, etc) as well as the compilers used (and versions)
and any hardware details you can. Perhaps someone can spot the problem.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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