On Mon, Apr 19, 2010 at 4:08 PM, XAvier Periole <x.peri...@rug.nl> wrote:
> > Hi, > > the rmsd you show is for the protein in vacuum? It goes up to 0.7 nm! That > is a very > large deformation, is it expected? Isn't your protein freezing and all the > kinetic energy > going into translational motion. > > there is a few things you could try. > 1- First you should increase the rlilst to at least 1.3 but 1.4 would be > better. > 2- And/or reduce the nstlist to 5. > > You should modify at least one of the two, that will increases the cost > of your simulation > but should make increase energy conservation. > > Then you should try a smaller time step 0.020 ps might just remove all the > lincs warnings. > > XAvier. > > I made all the modifications suggested, but the system still crashed (with segmentation fault). However, 'elastic bonds' representation that Martti suggested works and I may need these modifications later. Thanks for being so patient with my problem. > > > On Fri, Apr 16, 2010 at 5:17 PM, Martti Louhivuori > <m.j.louhivu...@rug.nl>wrote: > >> On 15 Apr 2010, at 18:06, Trang wrote: >> >>> My target system is a protein with lipid molecules added randomly (using >>> GENBOX). Running MD, I expect to >>> >> >> I hope you're using a larger van der Waals distance (0.24nm or so) when >> inserting the lipids. > > > I tried 0.3 - 0.5. It looked fine, but didn't work. > >> >> >> broke down the problem, that is, to run md simulation for the protein >>> molecule only, and in vacuum. Still no improvement. Although all the >>> distances in the minimized structure are visually proper, the system >>> exploded. >>> >> >> If you can't run the protein even in vacuum, then the problem is either in >> your MD parameters, starting co-ordinates or some simple mistake somewhere. >> Since the .mdp files you posted seem ok, my bet is on the starting >> co-ordinates, just as Xavier proposed. >> >> Could you post the system topology (.top) and the protein topology (.itp), >> so we can rule out any mistakes in those? > > > The protein topo is too large, so I put it here. http://pastie.org/926617 > Here is the system topology. > > ---------------------------- > #include "../martini_v2.1.itp" > #include "../martini_v2.1_aminoacids.itp" > #include "11BHSD1.itp" > > ; Include Position restraint file > #ifdef POSRES > #include "posre.itp" > #endif > > > [ system ] > 11BHSD1 > > [ molecules ] > 11BHSD1 1 > ---------------------------- > > > >> You should also double check whether you have close contacts between some >> atoms in the protein; e.g. in VMD this is easily done using the "dynamic >> bonds" representation. > > >> -martti- >> > > Minimized structure showed no close contact (with distance cutoff 1.6, even > to 1.9). Production run stopped at step 175552 (5266.56 ps) with > Segmentation fault, preceeded with a lot of Lincs warnings (I set ring_bonds > = "constraints"). This is the mdp file, this file goes along with the > system in vaccuum that crashed. I'm not sure if too long simulation time can > be the cause. The strange thing is that the system seemed to be relatively > stable at the time of crash. rmds.xvg is below, in case you want to see the > graph first-hand. > > -------------------------MD--------------------------- > integrator = md > tinit = 0.0 > dt = 0.030 > nsteps = 900000 > nstcomm = 1 > comm-grps = > nstxout = 5000 > nstvout = 5000 > nstfout = 0 > nstlog = 2000 > nstenergy = 2000 > nstxtcout = 1000 > xtc_precision = 100 > xtc-grps = > energygrps = > nstlist = 10 > ns_type = grid > pbc = xyz > rlist = 1.2 > coulombtype = Shift > rcoulomb_switch = 0.0 > rcoulomb = 1.2 > epsilon_r = 15 > vdw_type = Shift > rvdw_switch = 0.9 > rvdw = 1.2 > DispCorr = No > tcoupl = Berendsen > tc-grps = Protein > tau_t = 0.3 > ref_t = 323 > Pcoupl = berendsen > Pcoupltype = isotropic > tau_p = 3.0 > compressibility = 3e-5 > ref_p = 1.0 > gen_vel = no > gen_temp = 323 > gen_seed = 666 > constraints = none > constraint_algorithm = Lincs > unconstrained_start = no > lincs_order = 4 > lincs_warnangle = 30 > ---------------------------------------------------------- > > -------------rmsd.xvg------------------------------- > @ title "RMSD" > @ xaxis label "Time (ps)" > @ yaxis label "RMSD (nm)" > @TYPE xy > @ subtitle "Protein after lsq fit to Protein" > 0.0000000 0.0001400 > 150.0000000 0.6150032 > 300.0000000 0.6162945 > 450.0000000 0.6451609 > 600.0000000 0.6317724 > 750.0000000 0.6501579 > 900.0000000 0.6642945 > 1050.0000000 0.6742513 > 1200.0000000 0.6651280 > 1350.0000000 0.6965100 > 1500.0000000 0.6856629 > 1650.0000000 0.7271055 > 1800.0000000 0.7174531 > 1950.0000000 0.7088170 > 2100.0000000 0.7492073 > 2250.0000000 0.7352809 > 2400.0000000 0.7196461 > 2550.0000000 0.7162255 > 2700.0000000 0.7277457 > 2850.0000000 0.7121301 > 3000.0000000 0.7084662 > 3150.0000000 0.7153199 > 3300.0000000 0.7209989 > 3450.0000000 0.7342823 > 3600.0000000 0.7297466 > 3750.0000000 0.7254455 > 3900.0000000 0.7175814 > 4050.0000000 0.7134616 > 4200.0000000 0.7212958 > 4350.0000000 0.7258847 > 4500.0000000 0.7201833 > 4650.0000000 0.7286560 > 4800.0000000 0.7188574 > 4950.0000000 0.7177775 > 5100.0000000 0.7247230 > 5250.0000000 0.7153631 > ----------------------------------------------------------- > > > -- > 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 > > > > -- > 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 >
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