Alex Seling wrote:
Given the unfavorable input, then, it seems odd then that the same .mdp
and protein ran consistently on 4.0.7, and I can't seem to find anything
in the changelog to indicate a relevant change.
There are numerous algorithmic changes in the 4.5.x series. Many people have
reported the same problem you have (something works in 4.0.x and not 4.5.x) and
the solution is to set nsttcouple (and, if applicable, nstpcouple) to 1 for an
initial equilibration phase. The default is to have nsttcouple = nstlist,
which, in your case, is very infrequent.
Then, once the system is relaxed, you can remove this (very) frequent updating.
The coupling algorithms in 4.0.x were more relaxed, such that a system that
was not necessarily well-optimized might have had better odds of "working" (i.e.
surviving), but as I understand it, the new algorithms are, overall, more robust.
-Justin
On Thu, Jan 26, 2012 at 1:26 AM, Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> wrote:
On 26/01/2012 5:10 PM, Alex Seling wrote:
Hello,
After upgrading to gromacs 4.5.5, the old .mdp file that was
working is now giving me errors.
Marginally stable numerical integration can work out, or not. Here,
you are using a time step that is not suitable for a simulation
lacking bond constraints. See section 6.5 of manual, for example. If
you really want infinite cut-offs, read 7.3.9. Normal practice to
avoid problems is to use an equilibration regime whose integration
scheme is more gentle than your simulation regime.
Mark
Specifically, I'm getting
"This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size"
for a few interactions, with each of them approaching inf.
This is with a good starting configuration. Any ideas as to the
error? My .mdp file is below.
Thanks,
Alex Seling
title = lea at 300K
cpp = /lib/cpp -traditional
integrator = md ;sd ;md ;bd
tinit = 0.0
dt = 0.001 ;time step of 1 fs
nsteps = 238000000 ;1 us @ 1fs
nstxout = 200000 ; frequency to write coordinates to output
trajectory file = 1ns
nstxtcout = 200000 ; frequency to write coordinates to xtc
trajectory = 1 ns
nstvout = 0
nstfout = 0
nstlog = 200000 ; frequency to write energies to log file = 1 ns
nstenergy = 200000 ; frequency to write energies to energy file = 1ns
energygrps = system
comm_mode = angular
nstcomm = 40
nstlist = 100
nstype = simple
pbc = no
rlist = 100
rgbradii = 100
coulombtype = cut-off
epsilon_r = 1 ; double check this is what we want
rcoulomb = 100
vdwtype = cut-off
rvdw = 100
tc-grps = system
tau_t = 0.01099
ref_t = 300
gen_vel = yes
gen_temp = 273
constraints = none
implicit_solvent = GBSA
gb_algorithm = OBC
gb_epsilon_solvent = 78
--
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
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
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
========================================
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
========================================
--
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/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
