Dear gmx users,<br>I'm trying to run some CG-MD with gromacs, using the available Martini FF.<br>The first run with {lipid + water} is fine. The POPC lipid bilayer is successfully self-assembled. I then applied Martini FF for system involving protein.<br>
All the systems I've tried so far could not survive an md run for long enough. Most of them crashed at the very first step.<br><br>I've encountered different types of errors (range checking error, segmentation fault...) and even hanging of the system, all of which converge at the same suggestion that the system hasn't been minimized/equilibrated well enough.<br>
<br>I've tried some tracing back but still cannot figure out where the problem can be.<br><br>* From screen output, I traced back to the atoms on which large force affect: most of the cases, these atoms belong to the ring of amino acid such as TRP, TYR. The worst case was that, 2 beads of 1 TRP totally overlap after minimization!!! The newest trial is related to <a href="http://picasaweb.google.com/lh/photo/RMSyRH801u44-EiSQjK0-A?feat=directlink">atom 195 - 196 - 197, which are beads of the same TYR residue</a> . What kind of problem can cause such a bad minimization?<br>
<br>* From log file after crashed runs, I found the initial temperature is extremely high (e.g 6.67074e+12 K, etc). A colleague of mine suggest that it may be due to the high pressure, which in turn caused by unevenly distributed molecules in the input structure. This seemed to be reasonable, for after minimization (<a href="http://picasaweb.google.com/lh/photo/bSLh3oSC5VLxwRrmpeMecQ?feat=directlink">picture</a> ), the distribution of water is even worse than the initial state (<a href="http://picasaweb.google.com/lh/photo/qNEp0_FZdxiO05PqTVBsTw?feat=directlink">picture</a>). But, I get stuck and have no idea why minimization can make system so bad. This is the mdp for the minimization step<br>
-------------------------------MINI-----------------------------------------------<br>title = Martini<br>cpp = /usr/bin/cpp<br>integrator = steep<br>tinit = 0.0<br>
dt = 0.025<br>nsteps = 500<br>nstcomm = 1<br>comm-grps =<br>nstxout = 5000<br>nstvout = 5000<br>nstfout = 0<br>
nstlog = 1000<br>nstenergy = 1000<br>nstxtcout = 1000<br>xtc_precision = 100<br>xtc-grps =<br>energygrps =<br>nstlist = 10<br>
ns_type = grid<br>pbc = xyz<br>rlist = 1.2<br>coulombtype = Shift<br>rcoulomb_switch = 0.0<br>rcoulomb = 1.2<br>epsilon_r = 15<br>
vdw_type = Shift<br>rvdw_switch = 0.9<br>rvdw = 1.2<br>DispCorr = No<br>tcoupl = no<br>Pcoupl = no<br>gen_vel = no<br>
gen_temp = 320<br>gen_seed = 473529<br>constraints = none<br>constraint_algorithm = Lincs<br>unconstrained_start = no<br>lincs_order = 4<br>lincs_warnangle = 30<br>
------------------------------------------------------------------------------------<br><br><br>and this is for the next step md<br>------------------------------------MD--------------------------------------<br>title = Martini<br>
cpp = /usr/bin/cpp<br>integrator = md<br>tinit = 0.0<br>dt = 0.025<br>nsteps = 50000<br>nstcomm = 1<br>comm-grps =<br>
nstxout = 5000<br>nstvout = 5000<br>nstfout = 0<br>nstlog = 2000<br>nstenergy = 2000<br>nstxtcout = 1000<br>xtc_precision = 100<br>
xtc-grps =<br>energygrps =<br>nstlist = 10<br>ns_type = grid<br>pbc = xyz<br>rlist = 1.2<br>coulombtype = Shift<br>
rcoulomb_switch = 0.0<br>rcoulomb = 1.2<br>epsilon_r = 15<br>vdw_type = Shift<br>rvdw_switch = 0.9<br>rvdw = 1.2<br>DispCorr = No<br>
tcoupl = Berendsen<br>tc-grps = Protein W<br>tau_t = 0.3 0.3<br>ref_t = 323 323<br>Pcoupl = berendsen<br>Pcoupltype = isotropic<br>
tau_p = 3.0<br>compressibility = 3e-5<br>ref_p = 1.0<br>gen_vel = no<br>gen_temp = 323<br>gen_seed = 666<br>constraints = none<br>
constraint_algorithm = Lincs<br>unconstrained_start = no<br>lincs_order = 4<br>lincs_warnangle = 30<br>------------------------------------------------------------------------------------<br>
<br>I've struggled with this for about 2 weeks and still have no idea of where to fix the problem. Am I missing something too basic for tutorials to mention? I'm sorry for being such a newbie. I've tried my best to figure out the problem before asking for help. Can you give me some suggestions to get out of this?<br>