Dear all,<br><br> I am doing simulation of membrane protein for this I am following justin's tutorial In the first equilibration step i am getting error like this-<br>-------------------------------------------------------<br>
Program mdrun, VERSION 4.0.3<br>Source code file: trnio.c, line: 252<br><br>File input/output error:<br>Cannot write trajectory frame; maybe you are out of quota?<br><br>Can anyone have idea to solve this problem? If have please let me know.<br>
<br>My command line like this- <br><br>mdrun -v -s nvt.tpr -o new_seq-nvt.trr -c new_seq-nvt.gro -e newe_seq-nvt.edr -g new_seq-nvt.log.<br><br>My nvt.mdp file is below-<br><br>title = NVT equilibration for TAP-DMPC<br>
define = -DPOSRES ; position restrain the protein<br>; Run parameters<br>integrator = md ; leap-frog integrator<br>nsteps = 25000 ; 2 * 25000 = 50 ps<br>dt = 0.002 ; 2 fs<br>
; Output control<br>nstxout = 100 ; save coordinates every 0.2 ps<br>nstvout = 100 ; save velocities every 0.2 ps<br>nstenergy = 100 ; save energies every 0.2 ps<br>nstlog = 100 ; update log file every 0.2 ps<br>
; Bond parameters<br>continuation = no ; first dynamics run<br>constraint_algorithm = lincs ; holonomic constraints <br>constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrai<br>ned<br>
lincs_iter = 1 ; accuracy of LINCS<br>lincs_order = 4 ; also related to accuracy<br>; Neighborsearching<br>ns_type = grid ; search neighboring grid cels<br>nstlist = 5 ; 10 fs<br>
rlist = 1 ; short-range neighborlist cutoff (in nm)<br>rcoulomb = 1 ; short-range electrostatic cutoff (in nm)<br>rvdw = 1.2 ; short-range van der Waals cutoff (in nm)<br>
; Electrostatics<br>coulombtype = cut-off ; coulombtype cut-off<br>pme_order = 4 ; cubic interpolation<br>fourierspacing = 0.16 ; grid spacing for FFT<br>; Temperature coupling is on<br>
tcoupl = V-rescale ; modified Berendsen thermostat<br>tc-grps = Protein DMPC SOL_NA+ ; three coupling groups - more accurat<br>e<br>tau_t = 0.1 0.1 0.1 ; time constant, in ps<br>ref_t = 323 323 323 ; reference temperature, one for each <br>
group, in K<br>; Pressure coupling is off<br>pcoupl = no ; no pressure coupling in NVT<br>; Periodic boundary conditions <br>pbc = xyz ; 3-D PBC<br>; Dispersion correction<br>DispCorr = EnerPres ; account for cut-off vdW scheme<br>
; Velocity generation<br>gen_vel = yes ; assign velocities from Maxwell distribution<br>gen_temp = 323 ; temperature for Maxwell distribution<br>gen_seed = -1 ; generate a random seed<br>
<br>Thanks a lot in advance.<br><br>Nitu sharma<br><br>