The issue you are reporting has already been discussed (hint: search the
archives).
http://www.gromacs.org/pipermail/gmx-users/2007-July/028379.html
-Justin
Suman Chakrabarty wrote:
Dear developers,
could any of you please confirm whether one has to use certain general
thermostat in brownian dynamics (or stochastic dynamics) simulation or
"tcoupl = no" is justified? The manual says for stochastic dynamics
"the parameter tcoupl is ignored" (manual for ver. 4, page 141,
section 7.3.3). I would guess the same would be true for bd as well.
If "tcoupl = no" should be alright, then why the temperature obtained
from g_energy is almost double of the ref_t parameter? I have checked
this for a system consisting of a single polymer chain in vacuum.
If one has to use a general thermostat indeed, then please advise
which thermostat would be best appropriate for BD/SD simulations.
Thanks,
Suman.
On Fri, Apr 17, 2009 at 4:55 PM, Suman Chakrabarty
<su...@sscu.iisc.ernet.in> wrote:
On Fri, Apr 17, 2009 at 5:32 AM, Mark Abraham <mark.abra...@anu.edu.au> wrote:
Suman Chakrabarty wrote:
Hi,
it was pointed out before that for Brownian Dynamics simulation, the
temperature calculated by g_energy does not match with the ref_t in
parameter file and it is almost double:
http://www.gromacs.org/pipermail/gmx-users/2007-June/028321.html ...
but unfortunately I find no follow-up to that post.
So I want to ask the question again here. I am doing Brownian Dynamics
simulation of a single polymer chain consisting of 100 atoms. While I
have set 300K as my simulation temperature,
I don't think you have. You've generated velocities at that temperature, but
you're not thermostatting to that temperature, since you have "Tcoupl = no"
Are you sure? The manual says for stochastic dynamics "the parameter
tcoupl is ignored" (manual for ver. 4, page 141, section 7.3.3). I
would guess the same would be true for bd as well. For both sd and bd
there should be a different Langevin thermostat applicable, where the
temperature will be incorporated through the Gaussian distributed
random force term.
So I shall still need further clarification regarding this. Do I
really need to mention a general MD thermostat? Won't it be ignored as
mentioned for sd? If not, which thermostat is best for doing bd
simulations?
Regards,
Suman.
when I try to use g_energy
to check the temperature it reports the following:
Energy Average RMSD Fluct. Drift
Tot-Drift
-------------------------------------------------------------------------------
Temperature 624.188 44.0862 44.0862 -1.52693e-06
-0.152693
T-Protein 624.188 44.0862 44.0862 -1.52693e-06
-0.152693
Here is the content of my mdp file:
=============================================================================
integrator = bd
dt = 0.002 ; ps !
nsteps = 50000000 ; total 100 ns.
nstxout = 1000
nstvout = 0
nstfout = 0
nstlist = 10
nstlog = 100
rlist = 1.0
rvdw = 1.0
bd_fric = 0
ld_seed = -1
constraints = all-bonds
lincs_order = 8
lincs_iter = 8
Tcoupl = no
tau_t = 0.01
tc-grps = Protein
ref_t = 300
Pcoupl = no
gen_vel = yes
gen_temp = 300
gen_seed = 173529
=============================================
Please help me troubleshoot this problem. Thanks.
Best regards,
Suman Chakrabarty.
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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