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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