<br><br><div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername">rama david</b> <span dir="ltr"><<a href="mailto:ramadavidgroup@gmail.com">ramadavidgroup@gmail.com</a>></span><br>
Date: Fri, Mar 30, 2012 at 8:31 PM<br>Subject: About g_energy analysis<br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br><br><br>Hi Gromacs users , <br> <br>
I have 4 molecule in system, I am study how are they interacting ,<br>I did NPT, equilibration , for 1 ns with following MDP file..<br> <br>title = gromacs<br>define = -DPOSRES ; position restrain the protein<br>
; Run parameters<br>integrator = md ; leap-frog integrator<br>nsteps = 500000 ; 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 = 0.9 ; short-range neighborlist cutoff (in nm)<br>rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm)<br>
vdw-type = Cut-off<br>rvdw = 1.4 ; 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 = 310 310 ; 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> I used G96 53a6 force field , with spc water model<br><br>So I check system equilibriation I check press with g_energy <br>avg press = 1.17 avg density = 985.588 <br><br>Is system is equilibrated ??<br>And what other parameter are imp to check ???<br>
<br>I am new in these field so please all suggestion are welcome ..<br><br><br>Thank you in advance ...<br>
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