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.
Thanks Srinivas. On Fri, Apr 9, 2010 at 1:26 AM, Mark Abraham <mark.abra...@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 >> >> ++++++++++++++++++++++++++++++++ >> >> NOTE >> >> "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 > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- ********************************************* 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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