Denny Frost wrote:
Sorry about forgetting the simulation time. They run for about 12 ns,
at which point I stop them. They appear stable - the box vectors don't
change a lot (which is surprising since the pressure sure does). Below
is a complete mdp file.
If the box vectors aren't changing, then it's very odd that the pressure is not
a more acceptable value. What of the other parameters - temperature, energy,
etc? What type of energy minimization and/or equilibration did you do prior to
this run?
A few other notes:
title = Run1
cpp = /lib/cpp
constraints = all_bonds
integrator = md
dt = 0.004 ; ps !
Are you using virtual sites? If not, a 4-fs timestep may not be stable, even
with constraints.
nsteps = 20000000 ; total 4ns.
nstcomm = 1
nstxout = 50000
nstvout = 50000
nstfout = 0
nstlog = 5000
nstenergy = 5000
nstxtcout = 25000
nstlist = 10
ns_type = grid
pbc = xyz
coulombtype = PME
vdwtype = Shift
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
fourierspacing = 0.6
This fourierspacing is 5-6 times larger than what is generally considered
sufficiently accurate. Your PME term may be inaccurate if there are
insufficient grid points. If you're increasing the spacing for performance
reasons, you may be sacrificing accuracy.
;pme_order = 4
ewald_rtol = 1e-5
; Berendsen temperature coupling is on in two groups
Tcoupl = berendsen
tc_grps = BMI PF6
Are both of these groups large enough to warrant their own temperature coupling
groups?
http://www.gromacs.org/Documentation/Terminology/Thermostats
-Justin
tau_t = 0.1 0.1
ref_t = 300 300
nsttcouple = 1
; Energy monitoring
energygrps = BMI PF6
; Isotropic pressure coupling is now on
Pcoupl = berendsen
pcoupltype = isotropic
;pc-grps = BMI PFF
tau_p = 1.0
ref_p = 1.0
compressibility = 4.5e-5
; Generate velocites is off at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 100000
On Thu, Jan 20, 2011 at 3:49 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Denny Frost wrote:
from -1000 to 1000, depending on the system. The simulation box
is 8x8x8 nm (roughly) and contains about 12,000 atoms
Are the systems even stable? Is there a trend in the pressure, or
is it stable at those values? It seems that the systems are either
exploding or imploding. How long are the simulations? Can you post
a complete .mdp file?
-Justin
On Thu, Jan 20, 2011 at 3:09 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
Denny Frost wrote:
I am running a variety of NPT simulations with polar,
non-polar,
and ionic compounds. Although my results for density
agree well
with experimental values, the pressures I get from
g_energy are
off by 1 to 3 orders of magnitude. In the log file, the
pressure fluctuates around a lot from -400 to 400 bar, which
seems to be normal according to other posts on this list, but
the average (which is what g_energy gives me) is not 1.0
bar, as
I specified. Does anyone know how to correct this problem?
What is the average value you're getting? How long are your
simulations?
-Justin
Pressure coupling parameters:
Pcoupl = berendsen
pcoupltype = isotropic
tau_p = 1.0
ref_p = 1.0
compressibility = 4.5e-5
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
-- gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto: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>
<mailto: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 <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
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
