On 7/5/12 5:05 PM, jonas87 wrote:
I'm following the tutorial exactly. Even have my files named the same way.
The contents of my minil.mdp (pcb is changed from no to xyz right before
running the energy minimazation of the solvated system):
title = Energy Minimization ; Title of run
cpp = /lib/cpp ; Preprocessor
define = -DFLEXIBLE
integrator = steep ; Algorithm (steep = steepest descent
minimization)
emtol = 1.0 ; Stop minimization when the maximum force <
1.0 kJ/mol
nsteps = 500 ; Maximum number of (minimization) steps to
perform
nstenergy = 1 ; Write energies to disk every nstenergy steps
energygrps = System ; Which energy group(s) to write to disk
ns_type = simple ; Method to determine neighbor list (simple,
grid)
coulombtype = cut-off ; Treatment of long range electrostatic
interactions
rcoulomb = 1.0 ; long range electrostatic cut-off
rvdw = 1.0 ; long range Van der Waals cut-off
constraints = none ; Bond types to replace by constraints
pbc = no ; Periodic Boundary Conditions (yes/no)
You're probably losing the box information somewhere along the line while
switching back and forth between .gro and .pdb. The CRYST1 line in
protein-solvated.pdb should agree with the previous settings. If it doesn't,
something has gone wrong. I recall some previous version of Gromacs had issues
reading and writing correct box vectors in .pdb files; I don't know which one.
It's always safe to use .gro files for everything, though in principle, .pdb
files should work as well.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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
* Only plain text messages are allowed!
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
