Hello All, <br>I am having a weird problem and I do not know whether it has to do anything with Gromacs or the cluster setting I am using.<br>When I run a MD simulation (on any protein), the job automatically terminates overnight without an error message. I
mean if I start the job early in the morning it runs longer than if I
start the job later in the day. But it never runs to the desired length
mentioned in the .mdp file.<br><br>I am copying the .mdp file:<br><br>-----------------------------------------------------<br><br>integrator = md<br>nsteps = 5000000<br>dt = 0.002<br>nstlist = 10<br>
nstcomm = 1<br>rlist = 1.0<br>coulombtype = pme<br>rcoulomb = 1.0<br>vdw-type = cut-off<br>rvdw = 1.0<br>tcoupl = Nose-Hoover<br>tc-grps = protein non-protein<br>
tau-t = 0.5 0.5<br>ref-t = 298 298<br>Pcoupl = Parrinello-Rahman<br>pcoupltype = isotropic<br>tau_p = 1.0<br>compressibility = 4.5e-5<br>ref_p = 1.0<br>
nstxout = 100<br>nstvout = 100<br>nstxtcout = 100<br>nstenergy = 100<br>userint1 = 123<br>userint2 = 124<br>userint3 = 247<br>-----------------------------------------------------------<br>
<br>Any thoughts?<br><br>Sayan.<br clear="all"><br><br><br>