<br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div class="h5">
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Can you post the relevant .mdp file(s)? Are you preserving velocity information from the previous trajectory, or generating new velocities? Are any of the species in your system constrained?<br><font color="#888888">
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-Justin<br></font></blockquote><div><br><br>I usually use the final output file generated by GROMACS which contain the velocity. But, I dont preserve the velocity every timestep.<br><br>CNT, CMT are constrained. I would want to make them move only in X direction, but I cannot make the simulation work even when they are constrained.<br>
<br><br><br>title = Yo<br>cpp = /usr/bin/cpp<br>include = -I/home/rajesh/gromacs_forcefield/FMN<br>;include = -I/cygdrive/c/cygwin/gromacs_forcefield/FMN_force_field<br>define = <br>
<br>; RUN CONTROL PARAMETERS<br>integrator = md<br>tinit = 0 ; start time<br>dt = 0.002 ; time step<br>nsteps = 5000 ; number of steps<br>
init_step = 0 ; For exact run continuation or redoing part of a run<br>comm-mode = None ; mode for center of mass motion removal<br>nstcomm = 1 ; number of steps for center of mass motion removal<br>
comm-grps = ; group(s) for center of mass motion removal<br><br>; ENERGY MINIMIZATION OPTIONS<br>emtol = 100 ; Force tolerance<br>emstep = 0.1 ; initial step-size<br>
niter = 20000 ; Max number of iterations in relax_shells<br>fcstep = 0 ; Step size (1/ps^2) for minimization of flexible constraints<br>nstcgsteep = 1000 ; Frequency of steepest descents steps when doing CG<br>
nbfgscorr = 10<br><br>; OUTPUT CONTROL OPTIONS<br>nstxout = 100 ; coordinates<br>nstvout = 0 ; velocities<br>nstfout = 0 ; forces<br>
nstcheckpoint = 10000 ; Checkpointing helps you continue after crashes<br><br>nstlog = 100 ; Output frequency for energies to log file<br>nstenergy = 1000 ; Output frequency for energies to energy file<br>
nstxtcout = 00 ; Output frequency for xtc file<br>xtc-precision = 10000 ; Output precision for xtc file<br><br>; This selects the subset of atoms for the xtc file. You can<br>
xtc-grps = FMN SOD ; select multiple groups. By default all atoms will be written.<br>energygrps = FMN CNT SOD CMT SOL ; Selection of energy groups<br><br>; NEIGHBORSEARCHING PARAMETERS<br>
nstlist = 10 ; nblist update frequency<br>ns_type = grid ; ns algorithm (simple or grid)<br>pbc = xyz ; Periodic boundary conditions: xyz (default), no (vacuum);; or full (infinite systems only)<br>
rlist = 1.4 ; nblist cut-off<br>domain-decomposition = no<br><br>; OPTIONS FOR ELECTROSTATICS AND VDW<br>coulombtype = PME ; Method for doing electrostatics<br>rcoulomb-switch =<br>
rcoulomb = 1.4<br>epsilon-r = 1 ; Dielectric constant (DC) for cut-off or DC of reaction field<br>vdw-type = switch ; Method for doing Van der Waals<br>rvdw-switch = 1.2 ; cut-off lengths<br>
rvdw = 1.4<br>DispCorr = EnerPres ; Apply long range dispersion corrections for Energy and Pressure<br>table-extension = 1 ; Extension of the potential lookup tables beyond the cut-off<br>
<br>fourierspacing = 0.12 ; Spacing for the PME/PPPM FFT grid<br><br>fourier_nx = 0 ; FFT grid size, when a value is 0 fourierspacing will be used<br>fourier_ny = 0<br>
fourier_nz = 0<br><br>; EWALD/PME/PPPM parameters<br>pme_order = 4<br>ewald_rtol = 1e-05<br>ewald_geometry = 3d<br>epsilon_surface = 0<br>optimize_fft = no<br><br><br>; OPTIONS FOR WEAK COUPLING ALGORITHMS<br>
<br>Tcoupl = nose-hoover ; Temperature coupling<br>tc-grps = System ; Groups to couple separately<br>tau_t = 0.1 ; Time constant (ps)<br>ref_t = 300 ; Reference temperature (K)<br>
<br>Pcoupl = no ; Pressure coupling<br>Pcoupltype = semiisotropic<br><br>tau_p = 0.5 0.0 ; Time constant (ps), compressibility (1/bar) and reference P (bar)<br>
compressibility = 4.5e-5 0.0<br>ref_p = 1.0 0.0<br><br>; GENERATE VELOCITIES FOR STARTUP RUN<br>gen_vel = no<br>gen_temp = 300<br>gen_seed = 1993<br><br>; OPTIONS FOR BONDS<br>constraints = none<br>
constraint-algorithm = lincs ; Type of constraint algorithm<br>unconstrained-start = no ; Do not constrain the start configuration<br>Shake-SOR = no ; Use successive overrelaxation to reduce the number of shake iterations<br>
shake-tol = 1e-04 ; Relative tolerance of shake<br>lincs-order = 4 ; Highest order in the expansion of the constraint coupling matrix<br><br>; Number of iterations in the final step of LINCS. 1 is fine for<br>
; normal simulations, but use 2 to conserve energy in NVE runs.<br>; For energy minimization with constraints it should be 4 to 8.<br>lincs-iter = 1<br>lincs-warnangle = 30 ; Lincs will write a warning to the stderr if in one step a bond rotates over more degrees than<br>
morse = no ; Convert harmonic bonds to morse potentials<br><br>; ENERGY GROUP EXCLUSIONS<br><br>energygrp_excl = CNT CNT CMT CMT ; Pairs of energy groups for which all non-bonded interactions are excluded<br>
<br><br>; Dihedral angle restraints: No, Simple or Ensemble<br>dihre = No<br>dihre-fc = 1000<br>dihre-tau = 0<br>nstdihreout = 100 ; Output frequency for dihedral values to energy file<br>
<br>; Non-equilibrium MD stuff<br>acc-grps = <br>accelerate = <br>freezegrps = CNT CMT <br>freezedim = Y Y Y Y Y Y <br>cos-acceleration = 0 <br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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</font><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">
Thanks<br>
Rajesh<br>
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<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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