jampani srinivas wrote:
Dear Justin,
Thanks for your responce. Here is my mdp file.
+++++++++++++++++++++++++++++++++++++++
title = AB2130
cpp = /usr/bin/cpp
constraints = all-bonds
integrator = md
dt = 0.004 ; ps !
nsteps = 25000000 ; total 100.0 ns.
nstcomm = 1
nstxout = 1000 ; collect data every 2.0 ps
nstvout = 1000 ; collect velocity every 2.0 ps
nstfout = 0
nstlog = 0
nstenergy = 1000 ; collect energy every 2.0 ps
nstlist = 10
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
rvdw = 1.0
rvdw_switch = 0.9
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in two groups
Tcoupl = V-rescale
tau_t = 0.1 0.1
tc-grps = Tmp1 Tmp2
ref_t = 283.0 0.0
gen_vel = yes
gen_temp = 283.0
acc_grps = Tmp1
accelerate = 0.1 0.1 0.1
gen_seed = 181726
freezegrps = Tmp2
freezedim = Y Y Y
++++++++++++++++++++++++++++++++++++++++++++++++
There are a whole host of reasons that you're seeing an energy drift. Perhaps
you should give a more detailed description of what you're trying to do. Per
your original message, you imply that you have a very simple system of some
frozen and non-frozen group, which is clearly oversimplified. A few thoughts:
1. You're applying constant acceleration, so you're introducing non-equilibrium
conditions. What is Tmp1? Could it be working against Tmp2 (frozen) in some
way that is causing a clash?
2. You're not using energrygrp_excl for your frozen group. Per the manual:
"To avoid spurious contributions to the virial and pressure due to large forces
between completely frozen atoms you need to use energy group exclusions, this
also saves computing time."
3. Are you using virtual sites in addition to constraints? Does a shorter
timestep alleviate the energy drift? Have a look at the Gromacs 4 paper for
notes about use of virtual sites and constraints, and the effect on what's
reasonable for the time step.
I'd suggest working through this systematically - you've got a ton of variables
that could be opposing one another. Introduce them one at a time to see where
your system starts to break down.
-Justin
Thanks
Srinivas.
On Thu, Apr 8, 2010 at 7:52 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
jampani srinivas wrote:
Hi
Thanks for your response, I am allowing the two groups (frozen
and non-frozen) groups interact each other, i guess i am getting
the energy of total system from g_energy.
I checked the velocities of frozen group atoms, they are not
"zero". I have seen in git master that this problem was fixed
and updated in md.c file, I have downloaded this from git master
and compiled my gromacs again still i found that frozen atoms
gets the initial velocity.
I am not at all clear why the energy of system should blow up,
can you please help me if there is solution for this.
I haven't been following this closely; can you post an .mdp file?
-Justin
Thanks in advance.
Srinivas.
On Wed, Apr 7, 2010 at 4:47 PM, ms <deviceran...@gmail.com
<mailto:deviceran...@gmail.com> <mailto:deviceran...@gmail.com
<mailto:deviceran...@gmail.com>>> wrote:
jampani srinivas ha scritto:
> Dear Berk,
>
> I am sorry if i am confusing you with my poor description
of problem,
> actually I have submitted simulation with two temperature
coupling groups (i
> think you already know that from our earlier
conversations) and
found that
> there is a continuous increase in the total energy of the
system.
I could
> not observe any blowing in the output file but the system
energy is
> continuously increasing, i am using 4fs time step here.
Can you
please let
> me know if i have to give more details?
>
Which part of the system is increasing its energy?
m.
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*********************************************
J. Srinivasa Rao
Post-doctoral Research Associate
C/o Prof. Luis R Cruz Cruz
Computational Biophysics Group
Department of Physics
Drexel University
3141 Chestnut St
Philadelphia, PA 19104, USA.
Ph: Off: 215-895-1989
Mob: 704-706-4191
Web:http://jsrao.web.officelive.com/default.aspx
**********************************************
--
========================================
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
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*********************************************
J. Srinivasa Rao
Post-doctoral Research Associate
C/o Prof. Luis R Cruz Cruz
Computational Biophysics Group
Department of Physics
Drexel University
3141 Chestnut St
Philadelphia, PA 19104, USA.
Ph: Off: 215-895-1989
Mob: 704-706-4191
Web:http://jsrao.web.officelive.com/default.aspx
**********************************************
--
========================================
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
========================================
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