[gmx-users] problem with total energy
jampani srinivas
jampanis at gmail.com
Fri Apr 9 05:25:11 CEST 2010
Dear Justin,
I am sorry for the poor description of the problem, OK let me explain you
clearly here.
I have taken a decapeptide and solvated it with box size 6.0 nm, I want to
create a frozen wall (confined sphere) around protein after a certain radius
(in this case it is 2.5 nm). To achieve this i made two temperature coupling
groups, first (Tmp1) one has protein and waters within 2.5nm from the center
of the box and rest is second temperature coupling group (Tmp2). Initially
when i run the simulation it was creating nrdf = 0 for both groups, Berk has
helped me with a file readir.c file, i compiled my gromacs again that
problem was solved. I have submitted simulations again and found that the
energy was blowing up. I think you know the story after this. Earlier I want
protein to interact with inner wall of the frozen group and check what
happens, because of this I have never looked at the energygrps_excl option.
I have done with both 2 and 4 fs time steps and I took 4fs option to speed
up the simulation, and I have to still look at the paper you suggested me.
Thanks for your suggestions, I have implemented your suggestion one after
the other, finally when i use the energygrps_excl option it worked out. Now
there is no sudden drift in the energy, and also i checked the velocities of
non-frozen group is mostly zero (except for first frame)
When I use the energygrps_excel option in the following way i am getting the
below mentioned note i have to still understand what is this message. On the
other hand if i use only "energygrp_excl = Tmp2 Tmp2 Tmp2 Tmp1" line in
mdp file i am getting fatal error. Is it necessary to to define the energy
groups first and later exclude the energy option?
+++++++++++++++++++++++++++++
energygrps = Tmp1 Tmp2
energygrp_excl = Tmp2 Tmp2 Tmp2 Tmp1
++++++++++++++++++++++++++++++++
NOTE
"Can not exclude the lattice Coulomb energy between energy groups"
I used -maxwarn option here and generated the tpr file. I hope this does not
harm the simulation.
Please let me know your comments and suggestion.
Thanks very much for your kind help.
Srinivas.
On Thu, Apr 8, 2010 at 8:21 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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.
>> 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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
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> Please search the archive at http://www.gromacs.org/search before posting!
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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
**********************************************
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