Below is my .mdp file. The timestep dt shows as 0.001 ps<br><br clear="all">title = protein<br>
cpp = /lib/cpp<br>
; RUN CONTROL<br>
integrator = md<br>
nsteps = 3000000<br>
dt = 0.001<br>
; NEIGHBOR SEARCHING<br>
nstlist = 10<br>
ns_type = grid<br>
pbc = xyz<br>
rlist = 0.9<br>
; OUTPUT CONTROL<br>
nstxout = 500<br>
nstvout = 500<br>
nstxtcout = 0<br>
nstlog = 10<br>
constraints = all-bonds<br>
nstenergy = 100<br>
; OPTION FOR ELECTROSTATIC AND VDW<br>
coulombtype = PME<br>
rcoulomb_switch = 0<br>
rcoulomb = 0.9<br>
; Dielectric constant (DC) for cut-off or DC of reaction field<br>
epsilon_r = 1<br>
; Method for doing Van der Waals<br>
vdw-type = Cut-off<br>
; cut-off lengths<br>
rvdw_switch = 0<br>
rvdw = 0.9<br>
; Apply long range dispersion corrections for Energy and Pressure<br>
DispCorr = No<br>
; Extension of the potential lookup tables beyond the cut-off<br>
table-extension = 2.5<br>
; Spacing for the PME/PPPM FFT grid<br>
fourierspacing = 0.28<br>
; FFT grid size, when a value is 0 fourierspacing will be used<br>
fourier_nx = 0<br>
fourier_ny = 0<br>
fourier_nz = 0<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>
; OPTIONS FOR WEAK COUPLING ALGORITHMS<br>
tcoupl = V-rescale<br>
tc_grps = SOL Protein Na<br>
tau_t = 0.1 0.1 0.1<br>
ref_t = 300 300 300<br>
Pcoupl = Berendsen<br>
Pcoupltype = isotropic<br>
; Time constant (ps), compressibility (1/bar) and reference P (bar)<br>
tau_p = 1.0<br>
compressibility = 4.5e-5<br>
ref_p = 1.0<br>
gen_vel = yes<br>
gen_temp = 300<br>
<br>--<br>Chandan kumar Choudhury<br>NCL, Pune<br>INDIA<br>
<br><br><div class="gmail_quote">On Tue, Feb 16, 2010 at 11:27 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><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">On 17/02/10 04:43, Chandan Choudhury wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Thanks Justin !!<br>
But my state_prev.cpt file shows<br>
$gmxcheck -f state_prev.cpt<br>
<br>
Checking file state_prev.cpt<br>
<br>
# Atoms 186864<br>
Last frame -1 time 9346.700<br>
<br>
<br>
Item #frames Timestep (ps)<br>
Step 1<br>
Time 1<br>
Lambda 1<br>
Coords 1<br>
Velocities 1<br>
Forces 0<br>
Box 1<br>
<br>
Here also the time is greater than the .trr file.<br>
<br>
Cant understand how to overcome it.<br>
</blockquote>
<br></div>
Your checkpoint interval need not match your .trr-writing interval - see your .mdp file.<div class="im"><br>
<br>
Mark<br>
-- <br>
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