<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Dear gromacs users,<br>I ran a md simulation for 2ns with the mdp file as shown:<br>er spoel (236)<br>; Wed Nov 3 17:12:44 1993<br>; Input file<br>;<br>title = Yo<br>cpp = /usr/bin/cpp<br>constraints = all-bonds<br>integrator = md<br>dt = 0.002 ; ps !<br>nsteps = 5000 ; total 10
ps.<br>nstcomm = 1<br>nstxout = 250<br>nstvout = 1000<br>nstfout = 0<br>nstlog = 100<br>nstenergy = 100<br>nstlist = 10<br>ns_type = grid<br>rlist = 1.0<br>rcoulomb =
1.0<br>rvdw = 1.0<br>; Berendsen temperature coupling is on in two groups<br>Tcoupl = berendsen<br>tc-grps = Protein Non-Protein<br>tau_t = 0.1 0.1<br>ref_t = 300 300<br>; Energy monitoring<br>energygrps = Protein Non-Protein<br>; Isotropic pressure coupling is now on<br>Pcoupl =
berendsen<br>Pcoupltype = isotropic<br>tau_p = 0.5<br>compressibility = 4.5e-5<br>ref_p = 1.0<br>; Generate velocites is off at 300 K.<br>gen_vel = no<br>gen_temp = 300.0<br>gen_seed = 173529<br><br>it was successful, but then while using the trajectory convert; ie, to a xtc file and also while using g_rms and g_gyrate command, it got killed. So i modified the mdp file and re-ran the md simulation for 2ns; the mdp file is:<br>er spoel (236)<br>; Wed Nov
3 17:12:44 1993<br>; Input file<br>;<br>title = Yo<br>cpp = /usr/bin/cpp<br>define = -DPOSRES<br>constraints = all-bonds<br>integrator = md<br>dt = 0.002 ; ps !<br>nsteps = 1000000 ; total 2 ns.<br>nstcomm =
1<br>nstxout = 2500<br>nstvout = 2500<br>nstfout = 100<br>nstlog = 1000<br>nstenergy = 10<br>nstlist = 10<br>ns_type = grid<br>rlist = 1.0<br>rcoulomb = 1.0<br>rvdw =
1.0<br>; Berendsen temperature coupling is on in two groups<br>Tcoupl = berendsen<br>tc-grps = Protein Non-Protein<br>tau_t = 0.1 0.1<br>ref_t = 300 300<br>; Energy monitoring<br>energygrps = Protein Non-Protein<br>; Pressure coupling is not on<br>Pcoupl = no<br>tau_p = 0.5<br>compressibility =
4.5e-5<br>ref_p = 1.0<br>; Generate velocites is on at 300 K.<br>gen_vel = yes<br>gen_temp = 300.0<br>igen_seed = 173529<br><br>But still it was getting killed; ie, the xtc, and xvg file conversions.<br>Please help as to how i can overcome this problem.<br>thank you<br></td></tr></table><br>
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