The problem is the combination of pbc=full and comm_mode = angular.
With pbc=xyz it will work.
We will add a check for this.
Anyhow, pbc=full is only useful when you have periodic molecules.
Berk.
From: "Paul Whitford" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[email protected]>
To: "[email protected]" <[email protected]>
Subject: [gmx-users] Periodic Boundary conditions
Date: Wed, 7 Nov 2007 16:41:48 -0800
I am running v3.3.2. I am running an RNA strand with a homemade potential.
When I run a single molecule in a periodic box, the system is fine until
one
nucleic acid crosses the boundary. THen the entire nucleic acid gets moved
to the opposite side of the box. Since there are bonds this results in an
exploding system. I am running on 4 processors and am using the following
mdp file. Any ideas what is going on? The system runs normally for over
200000 time steps. It runs fine until the boundary issue occurs.
title = Paul Template
;Preprocessor
cpp = cpp
;Run control: A leap-frog algorithm for integrating Newton's equations.
integrator = sd
:time step in femtoseconds
dt = 0.0005
;number of stepsi
nsteps = 10000000
;frequency to write coordinates to output trajectory file
nstxout = 0
;frequency to write velocities to output trajectory file
nstvout = 0
;frequency to write energies to log file
nstlog = 1000
;frequency to write energies to energy file
nstenergy = 1000
;frequency to write coordinates to xtc trajectory
nstxtcout = 1000
;group(s) to write to xtc trajectory
xtc_grps = system
;group(s) to write to energy file
energygrps = system
;Frequency to update the neighbor list (and the long-range forces,
;when using twin-range cut-off's).
nstlist = 50
coulombtype = Cut-off
;Make a grid in the box and only check atoms in neighboring grid cells
;when constructing a new neighbor list every nstlist steps.
ns_type = grid
;cut-off distance for the short-range neighbor list
rlist = 2.5
;treatment of electrostatic interactions
table_extension = 150.0
rcoulomb = 2.5
epsilon_r = 0
;treatment of van der waals interactions
rvdw = 2.5
; Periodic boudary conditions in all the directions
pbc = full
;Temperature coupling
tc-grps = system
tau_t = 10.0
ref_t = 100
;Pressure coupling
Pcoupl = no
;Velocity generation
gen_vel = yes
gen_temp = 100
gen_seed = 12345
;Constrain all bonds
constraints = none
;constraint_algorithm = lincs
;lincs_iter=8
comm_mode = angular
thanks
-Paul
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_________________________________________________________________
Talk with your online friends with Messenger
http://www.join.msn.com/messenger/overview
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
