<p>Hi Priya,</p>
<p>Does it help if you set</p>
<p>tcoupl = v-rescale</p>
<p>Please read the manual, follow a tutorial properly, and think about what you're doing and what you get out.</p>
<p>Cheers,</p>
<p>Tsjerk</p>
<p><blockquote type="cite">On Jan 7, 2012 8:54 AM, "priya thiyagarajan" <<a href="mailto:priya.thiyagarajan09@gmail.com">priya.thiyagarajan09@gmail.com</a>> wrote:<br><br>hello sir,<br><br>i followed lysozyme tutorial to do dynamics for my protein..<br>
<br>but at the end of NVT equilibration, my temperature is at 243K.. but i set 300K to my mdp file ..<br><br>mine is not getting equilibrium condition..<br>
<br> this is my nvt.mdp file<br><br><br>title =GROMOS43a1 lipopeptide NVT equilibration<br>define = -DPOSRES ; position restrain the protein<br>
; Run parameters<br>integrator = md ; leap-frog integrator<br>nsteps = 100000 ; 2 * 100000 = 200 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) constrained<br>lincs_iter = 1 ; accuracy of LINCS<br>lincs_order = 4 ; also related to accuracy<br>
; Neighborsearching<br>ns_type = grid ; search neighboring grid cells<br>nstlist = 5 ; 10 fs<br>rlist = 1.0 ; short-range neighborlist cutoff (in nm)<br>rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)<br>
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)<br>; Electrostatics<br>coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics<br>pme_order = 4 ; cubic interpolation<br>
fourierspacing = 0.16 ; grid spacing for FFT<br>; Temperature coupling is on<br>tcoupl = No ; modified Berendsen thermostat<br>tc-grps = DRG SOL ; two coupling groups - more accurate<br>
tau_t = 0.1 0.1 ; time constant, in ps<br>ref_t = 300 300 ; reference temperature, one for each 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 = 300 ; temperature for Maxwell distribution<br>gen_seed = -1 ; generate a random seed<br><br><br>may i know what is the reason..<br><br>initially i did nvt for 100ps but i didnt get equil temperature.<br>
then i increased my time to 200ps.. still i am not getting..<br><br><br><br><br>help me with your answer..<br>
<br>Thanking you,
<br>--<br>
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