Sorry I forgot to attach my mdp files. Here is the mdp file for pulling simulaition: ------------------------------------------------------------------------- title = Martini cpp = /usr/bin/cpp define = -DPOSRES_LIP
integrator = md ; start time and timestep in ps tinit = 0.0 dt = 0.02 nsteps = 5000000 ; number of steps for center of mass motion removal = nstcomm = 10 comm-grps = nstxout = 5000 nstvout = 500000 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 1000 nstenergy = 1000 ; Output frequency and precision for xtc file = nstxtcout = 1000 xtc_precision = 100 nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ; Periodic boundary conditions: xyz or none = pbc = xyz ; nblist cut-off = rlist = 1.4 coulombtype = PME rcoulomb = 1.4 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon_r = 15 ; Method for doing Van der Waals = vdw_type = Shift ; cut-off lengths = rvdw_switch = 0.9 rvdw = 1.2 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = No ; Temperature coupling = tcoupl = V-rescale ; Groups to couple separately = tc-grps = Protein_lipid Sol_Ion ; Time constant (ps) and reference temperature (K) = tau_t = 1.5 1.5 ref_t = 310 310 ; Pressure coupling = Pcoupl = Parrinello-Rahman Pcoupltype = semiisotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau_p = 10.0 10.0 compressibility = 3e-5 3e-5 ref_p = 1.0 1.0 constraints = none ; Type of constraint algorithm = constraint_algorithm = Lincs ; Do not constrain the start configuration = unconstrained_start = no ; Highest order in the expansion of the constraint coupling matrix = lincs_order = 4 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs_warnangle = 90 ; pull staff ; pull staff pull = umbrella pull_geometry = position pull_vec1 = 0 0 -1 pull_dim = N N Y pull_start = no ; define initial COM distance > 0 pull_ngroups = 1 pull_group0 = lipid1 pull_group1 = Protein pull_init1 = 0.0 0.0 4.50 pull_rate1 = 0.001 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 ================================================================ Here is the pull part of the mpd file for the windowed umbrella sampling simulation, other part of the mdp file are same as that of pulling simulation. -------------------------------------------------------------------------------- pull = umbrella pull_geometry = position pull_vec1 = 0 0 -1 pull_dim = N N Y pull_start = no ; define initial COM distance > 0 pull_ngroups = 1 pull_group0 = lipid1 pull_group1 = Protein pull_init1 = 0.0 0.0 1.2 pull_k1 = 1000 ; kJ mol^-1 nm^-2 Cheers, Jianguo ________________________________ From: Jianguo Li <ljg...@yahoo.com.sg> To: jalem...@vt.edu; Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Tuesday, 22 February 2011 14:27:34 Subject: Re: [gmx-users] Can g_wham support using different temperature for different windows? Thanks Justin and Chris and sorry for confusing interpretation. Let me make it more clear. My peptide is flexible Martini beads, and highly positively charged. My membrane is a mixture of negatively charged lipids (25%) and zitterionic lipids(75%). So there is strong electrostatic attraction between peptide and membrane. To get the PMF, I did the following: (1) I did pulling simulation along (0 0 -1) direction to pull my peptide across the membrane. Then I got different configurations corresponding to different windows along the reaction coordinates, which is the z-distance between peptide and membrane. This figure (http://www.flickr.com/photos/lijg/5467080971/) shows some of the configurations at certain reaction coordinates. (2) In each window, I used the corresponding configuration that generated by the pulling simulation as initial input and run umbrella sampling. The size of each window is 0.15 nm, but close to the bilayer cneter (e.g., -0.6<d<0.6), I have increased number of windows so that the width of the window is to be 0.05 or 0.1 nm, I also tried to use different force constant in these windows. From the figure (http://www.flickr.com/photos/lijg/5467080971/) , we can classify the peptide conformation to be either extended (interacting with two bilayers) or compact (interacting with only one bilayer). Ideally, the peptide conformation should be similar for d=x and d=-x. The problem is that the configuration of peptide is not symmetric with respect to the bilayer center. For example, the peptide configuration is compact at d=0.6 and d=0.9, but the peptide is extended at d=-0.6 and d=-0.9. This leads Hysteresis. If I use g_wham to generate PMF, then the PMF is not symmetric with respect to the bilayer center. Using more number of windows and different force constant did not remove the problem. In my opinion, at least in some windows, the peptide should sample both compact and extended structure. But what I found is that the windowed umbrella simulation depends on the initial peptide conformation. If the initial peptide conformation is compact, then after 100 ns, it is still compact; if the initial peptide in that window is extended, the final configuration is also extended. I also tried to run longer equilibrium time (e.g., 200 ns), but the problem still exists. My question is how to increase sampling of the peptide conformation? I just think of two choices: (1) use high temperature (e.g., 500K) at those bad windows. As I mentioned, I am wondering if g_wham can unbias the effect of using different temperatures in different windows. (2) use REMD in those bad windows. These need a lot of computational resources. Is there any other method to deal with the insufficient sampling? Any suggestions are welcome, thanks for your time reading this email! Cheers, Jianguo ________________________________ From: Justin A. Lemkul <jalem...@vt.edu> To: Gromacs Users' List <gmx-users@gromacs.org> Sent: Tuesday, 22 February 2011 11:13:05 Subject: Re: [gmx-users] Can g_wham support using different temperature for different windows? Jianguo Li wrote: > Thanks for your comments, Justin. > > Using timestep of 20 fs, in each window the simulation runs for 100 ns CG > time. >The pulling rate is 0.001 nm/ps. Is it too fast? > Let me clarify things, since I'm not convinced I understand your procedure. You generate a series of configurations with 0.001 nm/ps pulling, but then how many windows do you generate for independent simulations? What are your .mdp parameters during those windows? The pull rate should be 0 during the actual umbrella sampling, to restrain the peptide within the window. What force constant(s) do you use? > My system is a little different. My peptide is highly positively charged. The >NMR experiments show that the conformation of the peptide in water is very >dynamic, so I make it flexible without fixing any secondary structure in >Martini >model. As was discussed in the last few days, do not interpret changes in structure too directly when using MARTINI. It is not designed to faithfully mimic secondary structure changes. > In the membrane, 25% of the lipids are negatively charged, so there are very >strong electrostatic attraction between peptides and membrane. > > During the peptide approaching the membrane from the top, peptide can take >different configurations at different reaction coordinates. When pulling the >peptide into the membrane, the peptide takes relatively compact structure and >interacts with only the top leaflet until the distance becomes smaller than >0.45 >nm, after that the peptide becomes extended structure and interacts with both >leaflets. This extended structure remains until the distance becomes -1.05 nm. >Further pulling leads to compact structure and interacts only with the lower >leaflet. So the comformation of the peptide is not symmetric between the >center >of the bilayer, which leads to Hysteresis. It seems that there is a huge > I guess I'm confused here, too. The peptide is compact when interacting with the top leaflet, extended further in the membrane, then compact again when interacting with the lower leaflet. What's strange about that? > energy barrier for the peptide to translocate across the membrane because if >the initial conformation in a certain window is extended (interacting with >both >leaflets), then it remains extended. Similarly, it the initial conformation in >a >certain window is compact (interacting with only one leaflet), it will remain >compact. > I don't see how that is necessarily unexpected or problematic. Peptides will change conformation depending on their environment. If you want a static structure to cross the membrane (which may or may not represent reality) you'll have to introduce some kind of intramolecular restraints. -Justin > Any Suggestions of dealing with the highly charged system? > > Cheers, > Jianguo > > > ------------------------------------------------------------------------ > *From:* Justin A. Lemkul <jalem...@vt.edu> > *To:* Gromacs Users' List <gmx-users@gromacs.org> > *Sent:* Tuesday, 22 February 2011 09:58:36 > *Subject:* Re: [gmx-users] Can g_wham support using different temperature for >different windows? > > > > Jianguo Li wrote: > > Thanks Justin. > > I tried your suggestions by either increase more windows and change the >force constant, but it seems the samplings are still bad in some windows. When >I >did pulling in (0 0 1) direction and a reverse pulling in (0 0 -1) direction, >I >got different configurations at certain reaction coordinates. And the windowed >umbrella sampling seems depends strongly on the initial configurations in that >window. Therefore I got different PMFs using pulling in (0 0 1) direction and >reverse pulling in （0 0 -1) direction. > > > > How long are each of the simulations in each window? Sufficient sampling >should eliminate any configurational bias and/or hysteresis. Also, if the >pulling that sets up the initial configurations is done slowly enough, you >won't >see these problems. Sounds to me like you're pulling too fast or hard, such >that the system is not stable. > > > In my simulation, I exert constraints on phosphate atoms in z direction, > so >there is no lipid flip-flop and the membrane will be stable at high >temperatures. Then I am thinking of increasing temperature in those bad >windows >to enhance sampling... > > > > I don't know if I can make a convincing argument here, but intuitively, these >windows would be sampling in a different ensemble, so the free energy >landscape >in these windows would be discontinuous with any adjacent windows that are >done >at different temperatures, and perhaps the forces required to restrain your >peptide at a given COM distance will still result in a discontinuous PMF. I >would also suspect that g_wham can't handle this situation; it has a -temp >flag, >but it only takes one value. So if you construct your PMF curve using WHAM, >but >supply incorrect or inconsistent information, I certainly wouldn't believe the >result. > > I guess the main point is, there are tons of published demonstrations of >peptides and other molecules crossing a membrane with SMD and umbrella >sampling, >so it should be possible to generate stable configurations without any funny >tricks. > > -Justin > > > best regards, > > Jianguo > > > > > > > > ------------------------------------------------------------------------ > > *From:* Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>> > > *To:* Discussion list for GROMACS users <gmx-users@gromacs.org ><mailto:gmx-users@gromacs.org>> > > *Sent:* Tuesday, 22 February 2011 09:35:37 > > *Subject:* Re: [gmx-users] Can g_wham support using different temperature >for different windows? > > > > > > > > Jianguo Li wrote: > > > Dear all, > > > > > > I want to get the PMF of my peptide across the membrane bilayer. First > I >pulled my peptide across the membrane and then did windowed umbrella sampling >along the reaction coordinates which is the z-distance between peptide and >membrane. However, I found that sampling is not sufficient in some >windows(e.g., >around the center of the membrane). To enhance the sampling, I am thinking to >run the simulation in those windows at higher temperature (e.g., 500K), but >this >will introduce a bias. My question is: can g_wham remove the bias due to using >different temperatures in different windows? > > > > > > If g_wham cannot deal with the bias due to using different T, I may > need >to do REMD in those windows. But that will be very expensive computationally. >Anybody have an idea of enhancing sampling in those windows? > > > > > > Btw, I am using Martini CG model. > > > > > > Any suggestions will be highly appreciated, thank you! > > > > > > > A more straightforward approach is to (1) add more sampling windows or (2) >increase the force constant in regions where there's poor sampling, or perhaps >both. > > > > -Justin > > > > > Cheers, > > > Jianguo > > > > > > > -- ======================================== > > > > 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@gromacs.org ><mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org ><mailto:gmx-users@gromacs.org>> > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/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 ><mailto:gmx-users-requ...@gromacs.org> <mailto:gmx-users-requ...@gromacs.org ><mailto:gmx-users-requ...@gromacs.org>>. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > -- ======================================== > > 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@gromacs.org ><mailto:gmx-users@gromacs.org> > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/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 ><mailto:gmx-users-requ...@gromacs.org>. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- ======================================== 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@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
-- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
