Dear Justin and Users: Thank you for your fast reply.
First, I want to clarify the "entanglement", so I can get more accurate consult from you! :) Of course, the non-bonded interaction makes entanglement "among" polymer chains. However, "Entanglement" here means the "intra"chain (intramolecular) one. In other words, one chain polymer (having enough monomers inside, e.g. 1 chain polymer containing 20 monomers) can be entangled with itself. This is the reason that I gave force filed parameters related to the bond (stretch), angle, dihedral, and improper dihedral. This is also reason that I have suspected the topology file, which assign force field... In addition, I am putting my setting here. ==== Beginning ==== title = Poly cpp = /lib/cpp include = -I../top define = integrator = md dt = 0.002 nsteps = 500000 nstxout = 5000 nstvout = 5000 nstlog = 5000 nstenergy = 250 nstxtcout = 250 xtc_groups = System energygrps = System nstlist = 10 ns_type = grid rlist = 0.7 coulombtype = cut-off rcoulomb = 0.9 rvdw = 0.8 tcoupl = Berendsen tc-grps = carbon hydrogen energygrps = carbon hydrogen tau_t = 0.1 0.1 ref_t = 300 300 Pcoupl = Berendsen tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = no gen_temp = 300 gen_seed = 173529 constraints = all-bonds ==== Ends ==== Thank you, always! Sincerely, C. Kim On Sat, Mar 7, 2009 at 2:19 PM, Justin A. Lemkul <[email protected]> wrote: > > > Tree wrote: > >> Dear Users: >> >> >> Hello? >> As you might know, I am trying to simulate polymer chains with gromacs. >> Thanks to Justin's large help, I can build topology, which is the >> essential to actually run the MD. >> After getting the MD result, I have a serious question. >> >> For polymer, as same as the other biopolymers, I assigned potential >> parameters for 1) bond (stretch), 2) angle, 3) dihedral, 3) improper values. >> I believe the grompp was working well, because there was no error message >> at all. >> After doing a set of actual simulations with my tpr file (and I've checked >> the processed topology file), unfortunately I could not see any >> "entanglement" motion. >> That motion, I believe, should consist of bond, angle, dihedral, improper, >> as we see in protein simulations. >> >> > Entanglement between chains? That would be a result on nonbonded > interactions between (or among) the chains. > > In this case, would you please explain what I have done wrong...? >> I guessed that the processed force filed (generated by "grompp") could be >> a problem, but according to Justin's explanations I think it is okay. >> >> > The "processed" topology is not generating a problem, per se. Whether or > not the force field parameters you are using (i.e., those from OPLS-AA) are > appropriate or not is what is the real question. > > How long are you simulating? It may be a question of timeframe. To > equilibrate large polymers may take tens (if not hundreds) of nanoseconds. > Another source of error could be the parameters you are specifying in your > .mdp file. If you post that, we might be able to tell if there are any > errors or inappropriate settings. > > More than likely, this is a simple question of timeframe and appropriate > sampling, which is the inherent limitation in any MD simulation. > > -Justin > > Please help me! >> (Hopefully I am becoming more prepared for a real polymer simulation >> guy...) >> >> Thank you! >> >> >> Sincerely, >> >> C Kim >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> http://www.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 [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > ICTAS Doctoral Scholar > 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 [email protected] > http://www.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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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