Hi Justin, Many thanks for the advice. Cheers, Siavoush ________________________________
From: [EMAIL PROTECTED] on behalf of Justin A. Lemkul Sent: Wed 2008/02/20 07:20 ب.ظ To: Discussion list for GROMACS users Subject: RE: [gmx-users] unfolding a protein Quoting Siavoush Dastmalchi <[EMAIL PROTECTED]>: > Hi Justi, > > Thanks for the comments. Yes, I am showing MD ~.mdp file and I know that my > system is not neutral. I am not following the unfolding path and my intention > by unfolding the protein is to get a conformation which I could regard it as > one of the feasible unfolded conformations. > Do you think, not neutralizing the system will somehow prevent unfolding? I don't think the ions are the cause. I think your simulation time is way too short to be seeing unfolding. I mentioned the ions because simulating a charged system is not necessarily a real approximation of a physiological (or in vitro) system. The world does not bear a net charge! I would suggest adding counterions to neutralize the charge, and use PME instead of cut-off. I think it is more reliable, based on my experience. The cut-off method for calculating electrostatics is quicker, but I believe PME is more accurate. -Justin > > Cheers, Siavoush > > ________________________________ > > From: [EMAIL PROTECTED] on behalf of Justin A. Lemkul > Sent: Wed 2008/02/20 06:35 E.U > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] unfolding a protein > > > > Quoting Siavoush Dastmalchi <[EMAIL PROTECTED]>: > > > Hi there, > > > > > > > > I want to unfold a protein (hen egg white lysozyme) which has got 4 > disulfide > > bounds. I have tried 1 ns of MD at 400 K either in vacuum or hydrated form > > and it didn't unfold. I know it may need longer time, but it doesn't show > any > > sign of even starting to unfold. I think I am restraining the protein in > some > > way. Please see below the content of ~.mdp file that I use. > > My guess is that 1 ns is far too short to see any signs of unfolding. > Typically, we think of protein folding on the microsecond - second timescale, > so even if you speed things along by running your simulation at higher > temperature, you should be running tens of nanoseconds, if not 100 or more. > Check the literature to see what other people consider a reasonable time > scale. > > Also, what have you done in terms of minimization and equilibration? Are you > showing the production MD .mdp file? > > As far as "thinking" you are restraining your protein, these are things you > need > to be very sure of :-) Your topology likely specifies #include "posre.itp" > if > you include a "define" statement within your .mdp file (which I don't see), > so > I doubt you are restraining your protein in any way. > > > > > > > > > Would you please let me know how I could unfold a protein using an MD > > simulation? > > > > Do you think unfolding a water soluble protein in vacuum would be faster? > > Maybe, but what would it prove? > > As a side note, are you including counterions in your simulation? I don't > see > them incorporated into your tc-grps, so I'm wondering if you have an > electroneutral system. > > -Justin > > > > > > > > > Cheers, Siavoush > > > > > > > > cpp = /lib/cpp > > include = -I../top > > integrator = md > > dt = 0.002 > > nsteps = 500000 > > nstxout = 1000 > > nstvout = 1000 > > nstlog = 100 > > nstenergy = 100 > > nstxtcout = 100 > > xtc_grps = protein sol > > energygrps = protein sol > > nstlist = 10 > > ns_type = grid > > rlist = 0.8 > > coulombtype = cut-off > > rcoulomb = 1.4 > > rvdw = 1.4 > > pbc = xyz > > tcoupl = berendsen > > tc-grps = protein sol > > tau_t = 0.1 0.1 > > ref_t = 400 400 > > Pcoupl = berendsen > > Pcoupltype = isotropic > > tau_p = 1.0 > > compressibility = 4.5e-5 > > ref_p = 1.0 > > gen_vel = yes > > gen_temp = 400 > > gen_seed = 173529 > > constraints = all-bonds > > > > _______________________________________________ > > 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 > Department of Biochemistry > Virginia Tech > Blacksburg, VA > [EMAIL PROTECTED] | (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 > > > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (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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