<br><br><div class="gmail_quote">On Mon, Feb 20, 2012 at 7:32 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im"><br>
<br>
Steven Neumann wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Justin and Gmx Users,<br>
<br>
I run a pulling of my ligand away from my protein with the same mdp file and I obtained two different plots - Force vs time (The breaking point occured at different times with different force). Can you please explain?<br>
</blockquote>
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If you change the stiffness of the spring, you change the magnitude of the applied force. Thus, the behavior you see will occur either faster or slower, depending on the strength of the spring.<br>
<br>
-Justin<div><div class="h5"><br></div></div></blockquote><div><br>So how can I change the stiffness of my spring?<br><br>Steven <br></div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div><div class="h5">
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
My mdp file:<br>
<br>
title = Umbrella pulling simulation<br>
define = -DPOSRES_L<br>
; Run parameters<br>
integrator = md<br>
dt = 0.002<br>
tinit = 0<br>
nsteps = 250000 ; 0.5ns<br>
nstcomm = 10<br>
; Output parameters<br>
nstxout = 5000 ; every 10 ps<br>
nstvout = 5000<br>
nstfout = 500<br>
nstxtcout = 500 ; every 1 ps<br>
nstenergy = 500<br>
; Bond parameters<br>
constraint_algorithm = lincs<br>
constraints = all-bonds<br>
continuation = yes ; continuing from NPT<br>
; Single-range cutoff scheme<br>
nstlist = 5<br>
ns_type = grid<br>
rlist = 0.9<br>
rcoulomb = 0.9<br>
rvdw = 0.9<br>
; PME electrostatics parameters<br>
coulombtype = PME<br>
fourierspacing = 0.12<br>
fourier_nx = 0<br>
fourier_ny = 0<br>
fourier_nz = 0<br>
pme_order = 4<br>
ewald_rtol = 1e-5<br>
optimize_fft = yes<br>
; Temperature coupling is on<br>
tcoupl = V-rescale ; modified Berendsen thermostat<br>
tc_grps = Protein_LIG Water_and_ions ; two coupling groups - more accurate<br>
tau_t = 0.1 0.1 ; time constant, in ps<br>
ref_t = 298 298 ; reference temperature, one for each group, in K<br>
; Pressure coupling is on<br>
Pcoupl = Parrinello-Rahman<br>
pcoupltype = isotropic<br>
tau_p = 1.0 compressibility = 4.5e-5<br>
ref_p = 1.0<br>
; Generate velocities is off<br>
gen_vel = no<br>
; Periodic boundary conditions are on in all directions<br>
pbc = xyz<br>
; Long-range dispersion correction<br>
DispCorr = EnerPres<br>
; Pull code<br>
pull = umbrella<br>
pull_geometry = distance ; simple distance increase<br>
pull_dim = N N Y<br>
pull_start = yes ; define initial COM distance > 0<br>
pull_ngroups = 1<br>
pull_group0 = Protein<br>
pull_group1 = LIG182<br>
pull_rate1 = 0.016 ; 0.008 nm per ps = 8 nm per ns<br>
pull_k1 = 200 ; kJ mol^-1 nm^-2<br>
<br>
</blockquote>
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-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
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