Hello,<br><br>I am having problems in carrying out a NPT equilibration
of my system at 500 K.<br><br>System: A 5 nm cube with peptide, Li+ ions
and 2,5-dihydroxybenzoic acid anion.<br><br>NVT equilibration gives
expected results.<br>
<br>When I load the npt.gro file in VMD, its
seems as if the molecules have fragmented/vaporized.<br><br>nvt.mdp:<br><br>title
= hist NPT equilibration<br>define = -DPOSRES ; position restrain
the protein<br>
; Run parameters<br>integrator = md ; leap-frog integrator<br>nsteps
= 50000 ; 2 * 50000 = 100 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 ; Restarting after NVT<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 =
Protein Non-Protein ; two coupling groups - more accurate<br>tau_t
= 0.1 0.1 ; time constant, in ps<br>ref_t = 500 500 ;
reference temperature, one for each group, in K<br>
; Pressure coupling is on<br>pcoupl = Parrinello-Rahman ; Pressure
coupling on in NPT<br>pcoupltype = isotropic ; uniform scaling of box
vectors<br>tau_p = 2.0 ; time constant, in ps<br>ref_p = 1.0
; reference pressure, in bar<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><br><br>If I use the same exact system and run NVT and NPT
equilibration at 300 K, everything seems to be working.<br><br>What
could be going wrong at 500 K?<br>
<br>Thanks,<br><font color="#888888">Shivangi</font>