On Fri, Apr 16, 2010 at 5:17 PM, Martti Louhivuori <[email protected]>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 -----------------------------------------------------------
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