[gmx-users] problem with total energy

jampani srinivas jampanis at gmail.com
Fri Apr 9 16:17:15 CEST 2010

Dear Mark and Justin,

Thanks for your help, as a beginner to GROMACS i think i have to spend even
more time with each option and make sure i know what i am doing. I will
spend some time by using different electrostatic options with out pbc and
let you know what happens to the simulations.


On Fri, Apr 9, 2010 at 1:26 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> On 9/04/2010 1:25 PM, jampani srinivas wrote:
>> 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?
> Yes, energy group exclusions require matching energy group definitions. The
> relevant part of manual 7.3 probably says this.
>  +++++++++++++++++++++++++++++
>> energygrps     = Tmp1 Tmp2
>> energygrp_excl  = Tmp2 Tmp2 Tmp2 Tmp1
>> ++++++++++++++++++++++++++++++++
>> "Can not exclude the lattice Coulomb energy between energy groups"
> You seem to be trying to simulate a droplet inside a rigid shell of water.
> If so, why do you want the system to be periodic? You don't want periodicity
> artefacts *and* frozen-water-shell artefacts. There are other electrostatics
> models better suited than PME to such situations. You should look in the
> literature for successful published methodologies, rather than risk
> inventing a square wheel yourself before you've got enough experience to be
> confident with what you're doing.
> Here, the reciprocal-space part of the PME calculation must contain
> contributions from your excluded energy-groups, so you've got some
> Frankenstein possible worst-of-all-worlds combination. If I got such a paper
> to review, I'd need to see some serious groundwork justifying such a choice.
>  I used -maxwarn option here and generated the tpr file. I hope this does
>> not harm the simulation.
> That's a risky strategy. The programmer didn't put in such a message just
> to see whether he could do it...
> Mark
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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
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