Re: [gmx-users] Pulling in GROMACS 4.0.3
Hi again, I actually figured it out. Turns out, it was a stupid formatting error in the .mdp file. Even though I had it as shown, it didn't read the pull command because it wasn't formatted properly (thought it was still a part of the first line). Sorry guys. --Johnny > Hi Justin, > > Thx for the reply. By pull apart, I just wanted to expose an 'activation > site' by using a force. It is somewhat similar to pulling two domains of a > protein away from each other. I'm not aiming to undo any secondary > structure. I hope this is clearer. Thanks again! > > --Johnny > > >> >> >> Johnny Lam wrote: >>> Hi again, >>> >>> >>> I am trying to pull apart a CG protein (to verify CG results with those >>> of >>> already published works using atomistic MD). Using the previous >>> suggestions, my new pull code is the following: >>> >> >> By "pull apart," do you mean to unwind the secondary structure of the >> protein? >> If so, I don't think it will work. Doesn't MARTINI fix certain backbone >> parameters such that secondary structure remains very rigid over time? >> >> If that's the case, then the vibrations you're seeing are just the >> structure >> trying to resist being pulled apart. >> >> -Justin >> >> -- >> >> >> Justin A. Lemkul >> Ph.D. Candidate >> 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 >> >> >> > > > - > Johnny Lam > ISPE Berkeley Chapter External Vice President > Department of Bioengineering > College of Engineering > University of California, Berkeley > Tel: (408) 655- 6829 > Email: john...@berkeley.edu > > > - Johnny Lam ISPE Berkeley Chapter External Vice President Department of Bioengineering College of Engineering University of California, Berkeley Tel: (408) 655- 6829 Email: john...@berkeley.edu ___ gmx-users mailing listgmx-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
Re: [gmx-users] Pulling in GROMACS 4.0.3
Hi Justin, Thx for the reply. By pull apart, I just wanted to expose an 'activation site' by using a force. It is somewhat similar to pulling two domains of a protein away from each other. I'm not aiming to undo any secondary structure. I hope this is clearer. Thanks again! --Johnny > > > Johnny Lam wrote: >> Hi again, >> >> >> I am trying to pull apart a CG protein (to verify CG results with those >> of >> already published works using atomistic MD). Using the previous >> suggestions, my new pull code is the following: >> > > By "pull apart," do you mean to unwind the secondary structure of the > protein? > If so, I don't think it will work. Doesn't MARTINI fix certain backbone > parameters such that secondary structure remains very rigid over time? > > If that's the case, then the vibrations you're seeing are just the > structure > trying to resist being pulled apart. > > -Justin > > -- > > > Justin A. Lemkul > Ph.D. Candidate > 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 > > > - Johnny Lam ISPE Berkeley Chapter External Vice President Department of Bioengineering College of Engineering University of California, Berkeley Tel: (408) 655- 6829 Email: john...@berkeley.edu ___ gmx-users mailing listgmx-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
Re: [gmx-users] Pulling in GROMACS 4.0.3
Johnny Lam wrote: Hi again, I am trying to pull apart a CG protein (to verify CG results with those of already published works using atomistic MD). Using the previous suggestions, my new pull code is the following: By "pull apart," do you mean to unwind the secondary structure of the protein? If so, I don't think it will work. Doesn't MARTINI fix certain backbone parameters such that secondary structure remains very rigid over time? If that's the case, then the vibrations you're seeing are just the structure trying to resist being pulled apart. -Justin -- Justin A. Lemkul Ph.D. Candidate 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 listgmx-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
[gmx-users] Pulling in GROMACS 4.0.3
Hi again, I am trying to pull apart a CG protein (to verify CG results with those of already published works using atomistic MD). Using the previous suggestions, my new pull code is the following: title= Martini cpp = /usr/bin/cpp integrator = md ; start time and timestep in ps tinit= 0.0 dt = 0.030 nsteps = 2500 ; number of steps for center of mass motion removal = nstcomm = 1 comm-grps= ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 2500 nstvout = 2500 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 1000 nstenergy= 1000 ; Output frequency and precision for xtc file = nstxtcout= 33 xtc_precision= 100 ; This selects the subset of atoms for the xtc file. You can = ; select multiple groups. By default all atoms will be written. = xtc-grps = ; Selection of energy groups = energygrps = ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ; Periodic boundary conditions: xyz or none = pbc = xyz ; nblist cut-off = rlist= 1.4 ; Method for doing electrostatics = coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 ; 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 W ; Time constant (ps) and reference temperature (K) = tau_t= 0.3 0.3 ref_t= 323 323 ; Pressure coupling = Pcoupl = berendsen Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau_p= 3.0 compressibility = 3e-5 ref_p= 1.0 ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = no gen_temp = 323 gen_seed = 666 constraints = none ; Type of constraint algorithm = constraint_algorithm = SHAKE ; 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 = 60 ; FREEZE GROUP ; freezegrps = freeze ; freezedim = Y Y Y ; Pulling pull= umbrella pull_geometry = distance pull_start = yes pull_nstxout= 10 pull_nstfout= 10 pull_ngroups= 1 pull_group0 = freeze pull_group1 = pull pull_init1 = 0.0 0.0 0.0 pull_rate1 = 5000.0 pull_k1 = 100 The reason why the number of time steps is quite small, the pull_rate quite high, and the force constant low is because I wanted to verify that the code actually works before doing the actual production run (around 13 ns). The issue I'm running into is that when I check the results using VMD, it seems almost as if the simulation ignored all of my pull commands. I changed the rate, force constant, and the # timesteps to many different values but to no avail. Every result seems to indicate that my pull commands were not read (nothing happens aside from vibration). I highly doubt that there is a bug (as mentioned in an earlier post). I don't know why this is happening. Is there something wrong with the code? I really appreciate the help! --Johnny - Johnny Lam ISPE Berkeley Chapter External Vice President Department of Bioengineering College of Engineering University of California, Berkeley Tel: (408) 655- 6829 Email: john...@berkeley.edu ___ gmx-users mailing listgmx-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
