[gmx-users] problem with total energy
Justin A. Lemkul
jalemkul at vt.edu
Fri Apr 9 02:21:44 CEST 2010
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 <jalemkul at vt.edu
> <mailto:jalemkul at 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 <devicerandom at gmail.com
> <mailto:devicerandom at gmail.com> <mailto:devicerandom at gmail.com
> <mailto:devicerandom at 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.
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> **********************************************
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> --
> ========================================
>
> 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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