<div dir="ltr"><div><div>Hi. I'm trying to run NVE on a<br></div>~170 amino acid protein<br>with a harmonic dihedral angle restraint of 4184 kJ/mol rad^2,<br>in a rhombic dodecahedron water box that is 15 angstroms away from the protein<br>
using single precision gromacs,<br>and 0.5 fs time step.<br><br></div><div>Since I only want to get many short stretches of NVE simulations, I alternate npt and nve:<br><br></div><div>0. Steepest descent minimization with emtol = 1000.0.<br>
</div><div>1. [NVT equilibration, 2fs timestep 100,000 frames]<br>2. [NPT equilibration, 2fs timestep, 100,000 frames]<br>3. [NPT equilibration, 2fs timestep, 5,000 frames, Berendsen thermostat at 300K, position restraint?]<br>
</div><div>4. [NVE md,0.5 fs timestep, 35,000 frames, no thermostat]<br></div><div>5. go to step 3.<br><br></div><div>(all of these steps have the dihedral angle restraint)<br></div><div><br></div><div>In the NVE step, I get about 0.1% total energy decrease from start to end(figure). (the total energy keep dropping).<br>
But, the temperature still fluctuate in a range of ~ 5 Kelvin (<a href="http://oi60.tinypic.com/sni5at.jpg">figure</a>). Is that normal? Does that happen in real world? Where does this temperature fluctuation come from? How to reduce that? Does the restraint have anything to do with this?<br>
<img alt="Inline image 2" src="cid:ii_1480e99b16900d7b" height="532" width="466"><br><br><img alt="Inline image 1" src="cid:ii_1480e878b6faab35" height="532" width="432"><br><br></div><div>Below is the mdp file that I was using:<br>
<br>; Amber99SB MD <br>; Run parameters<br>integrator = md ; leap-frog integrator<br>nsteps = 32768 ; 2 * 100000 = 200 ps, 1 ns<br>dt = 0.0005 ; 1 fs<br>; Output control<br>nstfout = 2<br>
nstxtcout = 2 ; xtc compressed trajectory output every 2 fs<br>nstlog = 1000 ; update log file every 2 ps<br>xtc-grps=protein;<br><br>continuation = yes ; Restarting after NPT <br>constraint_algorithm = Lincs ; holonomic constraints <br>
constraints = h-bonds ; all bonds (even heavy atom-H bonds) constrained<br>lincs_iter = 2 ; accuracy of LINCS<br>lincs_order = 4 ; also related to accuracy<br>; Neighborsearching<br>ns_type = grid ; search neighboring grid cells<br>
nstlist = 10 ; 10 fs<br>rlist = 1.8 ; short-range neighborlist cutoff (in nm)<br>rcoulomb = 1.5 ; short-range electrostatic cutoff (in nm)<br>rvdw = 1.5 ; short-range van der Waals cutoff (in nm)<br>
; Electrostatics<br><br>coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics<br>pme_order = 6 ; cubic interpolation<br><br>fourierspacing = 0.12 ; grid spacing for FFT<br>optimize_fft = yes<br>
<br>tcoupl = no<br>pcoupl = no<br><br>compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1<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 = no ; Velocity generation is off <br>verlet-buffer-drift=-1<br>cutoff-scheme = Verlet;<br>
<br></div><div>Thanks again.<br></div></div>