<DIV> </DIV><DIV> </DIV><SPAN>On 29/02/12, <B class=name>"bo.shuang" </B><bs16@rice.edu> wrote:</SPAN>
<BLOCKQUOTE style="BORDER-LEFT: #00f 1px solid; PADDING-LEFT: 13px; MARGIN-LEFT: 0px" class=iwcQuote cite=mid:CA+4uorPDNpK93gQ8tbNKLr13SszRs_OfVu+pxD+cEXcb71GRVg@mail.gmail.com type="cite">Hi, all,<br /><br />I have a question about change the temperature in simulation. When I change the ref_t and gen_temp only, (from 300 to 400) I cannot see any difference. I am thinking if I need to change tau_t also, since diffusivity constant is also related to temperature. Am I right?<br /><br />Here is my mdp file:<br />title = OPLS Lysozyme NVT equilibration <br />;define = -DPOSRES ; position restrain the protein <br />; Run parameters <br />integrator = bd ; leap-frog integrator </BLOCKQUOTE>
<DIV> </DIV><DIV>By their nature, Browning and stochastic dynamics do not work with temperature coupling algorithms. IIRC gen_temp + gen_vel should have an effect on the initial conditions.</DIV><DIV> </DIV><DIV>Mark </DIV><DIV> </DIV><BLOCKQUOTE style="BORDER-LEFT: #00f 1px solid; PADDING-LEFT: 13px; MARGIN-LEFT: 0px" class=iwcQuote cite=mid:CA+4uorPDNpK93gQ8tbNKLr13SszRs_OfVu+pxD+cEXcb71GRVg@mail.gmail.com type="cite">
<DIV class="mimepart text html"><br />nsteps = 500000 ; 2 * 500000 = 1000 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 = yes ; 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 = V-rescale ; modified Berendsen thermostat <br />tc-grps = system ; two coupling groups - more accurate <br />tau_t = 0.01 ; time constant, in ps <br />ref_t = 400 ; 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 changed <br />gen_temp = 400 ; temperature for Maxwell distribution <br />gen_seed = 100 ; generate a random seed <br />ld_seed=-1 <br /><br /><br />Thank you!<br /><br />Bo<br /></DIV></BLOCKQUOTE>
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