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Dear Eric,
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I have attached my input parameters. Integration
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timestep is 0.5 fs and coupling time already 0.1 ps.
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I have also attached the beginning of the output
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of g_traj -f traj.trr -ot
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that shows the temperature falling down within
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the first picoseconds.
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What else can I change/check?
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Thanks for any help,
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Gitta
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;
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; MD Input File
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;
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;
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title = MD run at 371 K
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cpp = /lib/cpp
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; *** Run control ***
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integrator = md
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tinit = 0
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dt = 0.0005
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nsteps = 10000000
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nstcomm = 1
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comm_grps = ABc HOH
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; *** Output control ***
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nstxout = 100000
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nstvout = 100000
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nstfout = 0
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nstlog = 10000
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nstenergy = 10000
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nstxtcout = 10000
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; *** Neighbor searching ***
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nstlist = 10
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ns_type = grid
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pbc = xyz
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rlist = 1.2
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; *** Electrostatics and VdW
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coulombtype = Cut-off
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rcoulomb_switch = 0.0
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rcoulomb = 1.4
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epsilon_r = 1.0
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vdwtype = Cut-off
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rvdw_switch = 0.0
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rvdw = 1.4
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DispCorr = EnerPres
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; *** Temperature coupling ***
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tcoupl = Berendsen
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tc_grps = ABc HOH
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tau_t = 0.1 0.1
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ref_t = 371.0 371.0
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; *** Pressure coupling ***
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Pcoupl = Parrinello-Rahman
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Pcoupltype = isotropic
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tau_p = 1
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compressibility = 4.5e-5
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ref_p = 1
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; *** Velocity gerneration ***
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gen_vel = yes
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gen_temp = 371.0
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gen_seed = 173529
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; *** Bonds ***
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constraints = none
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unconstrained_start = yes
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# This file was created by g_traj
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# which is part of G R O M A C S:
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# Gravel Rubs Often Many Awfully Cauterized Sores
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# All this happened at: Thu Mar 20 13:57:30 2003
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#
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@ title "Temperature"
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@ xaxis label "Time (ps)"
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@ yaxis label "(K)"
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@TYPE xy
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@ view 0.15, 0.15, 0.75, 0.85
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@ legend on
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@ legend box on
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@ legend loctype view
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@ legend 0.78, 0.8
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@ legend length 2
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@ s0 legend "ABc"
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@ s1 legend "SOL"
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0 376.324 370.866
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50 345.259 249.622
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100 374.621 245.835
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150 417.497 247.743
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200 359.358 250.647
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>Hi,
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>Are you really using 1 femtosecond for the coupling time, or did you
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>mean 1 picosecond?
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>The values in the mdp file are given in picoseconds; if you don't get
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>the correct temperature
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>I would first try to use a shorter coupling time, say 0.1 picoseconds.
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>Cheers,
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>Erik
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On Wednesday, Mar 19, 2003, at 22:46 US/Pacific, B. Nick wrote:
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>
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> Dear all,
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>
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> I want to run a MD simulation of a 74 atoms
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> solute in 1600 SPC water molecules at 371 K.
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> I coupled each group (solute and solvent)
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> separately to the temperature control.
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> If I analyze the temperature after MD
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> I see that the solute is about 370 K whereas
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> the water cools down to 251 K during the
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> first ps of the run. This happens
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> irrespectively of the thermostat and timestep.
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> I used Berendsen and Nose-Hoover with a timestep
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> of 1fs or 0.5 fs.
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> Why isn't the temperature of both near 371 K?
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> Can anyone explain this to me?
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>
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> Thanks in advance,
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> Gitta
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>
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> --
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> Dr. Birgitta Nick
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> Deutsches Wollforschungsinstitut
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> Veltmanplatz 8, D-52062 Aachen, Germany
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-----
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Erik Lindahl, MSc, PhD <lindahl@stanford.edu>
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D109, Fairchild Building
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Dept. Structural Biology, Stanford University School of Medicine
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Tel. 650-7250754 Fax. 650-7238464
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