Hi!<br>Thanks for your reply.<br>I am having an on going simulation the md.log file states that it has written 875ps but the energy file data for only 662 ps!! this is brand new machine and is so there is no problem of running out of space. I am appending my pr.mdp file please take a look if its some thing to do with parameters and kindly suggest modifications if needed.<br>
Thanks<br>JJ<br>title = Yo<br>cpp = /usr/bin/cpp<br>define = -DDISRES<br>constraints = none<br>;constraint_algorithm = lincs<br>;lincs_order = 4<br>integrator = md<br>
dt = 0.001 ; ps !<br>nsteps = 1000000 ; total 1.0ns.<br>nstcomm = 1<br>nstxout = 5000<br>nstvout = 5000<br>nstfout = 5000<br>nstlog = 5000<br>
nstenergy = 5000<br>nstlist = 10<br>ns_type = grid<br>rlist = 1.0<br>coulombtype = PME<br>rcoulomb = 1.0<br>vdwtype = cut-off<br>rvdw = 1.4<br>
fourierspacing = 0.12<br>fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>pme_order = 4<br>ewald_rtol = 1e-5<br>optimize_fft = yes<br>disre = simple<br>
disre_weighting = equal<br>; Berendsen temperature coupling is on in two groups<br>Tcoupl = V-rescale<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 = parrinello-rahman<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>"pr.mdp" 52L, 1481C 38,1 Top<br>
<br><br><br><br><div class="gmail_quote">On Wed, Feb 25, 2009 at 11:03 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="Ih2E3d">jayant james wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi!<br>
I ran a simulation for 1ns (it was a continious run) and when I analyse the system energy, I find that the energy file has input till only 500pico seconds. Now that I want to extend my simulations I am in a fix!! What could be going wrong? I am using GMX version 3.3.3.<br>
</blockquote>
<br></div>
Maybe your file system became full, or your cluster file system was no longer accessible to the simulation node, or the simulation was interrupted before it completed flushing the buffers. Whatever happened, GROMACS did not terminate normally, because if there were any relevant .edr parameters to save at simulation end, it would have done so.<br>
<br>
If you consult the wiki, you will see some strategies for recovering from here.<br>
<br>
Mark<br>
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</blockquote></div><br><br clear="all"><br>-- <br>Jayasundar Jayant James<br><br><a href="http://www.chick.com/reading/tracts/0096/0096_01.asp">www.chick.com/reading/tracts/0096/0096_01.asp</a>) <br><br>