<div dir="ltr">Hi Justin,<br><br>Here is my complete code for umbrella sampling<br><br>title = Umbrella pulling simulation <br>define = -DPOSRES_2<br><br>integrator = md<br>dt = 0.002<br>tinit = 0<br>
nsteps = 2500000 ; 5 ns <br>nstcomm = 10<br>nstxout = 50000 ; every 100 ps<br>nstvout = 50000 <br>nstfout = 5000<br>nstxtcout = 5000 ; every 10 ps<br>nstenergy = 5000<br><br>constraint_algorithm = lincs<br>
constraints = all-bonds<br>continuation = yes<br><br>nstlist = 5<br>ns_type = grid <br>rlist = 1.4<br>rcoulomb = 1.4<br>rvdw = 1.4<br><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><br>; Berendsen temperature coupling is on in two groups<br>
Tcoupl = V-rescale<br>tc_grps = Protein SOL<br>tau_t = 0.5 0.5<br>ref_t = 300 300<br><br>; Pressure coupling is on<br>Pcoupl = Parrinello-Rahman <br>pcoupltype = isotropic<br>
tau_p = 1.0 <br>compressibility = 4.5e-5<br>ref_p = 1.0<br><br>; Generate velocities is off<br>gen_vel = no <br><br>; Periodic boundary conditions are on in all directions<br>pbc = xyz<br>
<br>; Long-range dispersion correction<br>DispCorr = EnerPres<br><br>; Pull code<br>pull = umbrella<br>pull_geometry = distance<br>pull_dim = N N Y<br>pull_start = yes <br>pull_ngroups = 1<br>
pull_group0 = Chain_B <br>pull_group1 = Chain_A <br>pull_init1 = 0<br>pull_rate1 = 0.0<br>pull_k1 = 1000 <br>pull_nstxout = 1000 <br>pull_nstfout = 1000 <br><br><br>I will do this umbrella sampling for 10ns, <br>
Do you think the COM distance can converge after long simulation time? ie back to the restraint position.<br><br>Regards,<br>Vijay.<br><br><br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
Vijayaraj wrote:<br>
> Hello,<br>
><br>
> I am doing umbrella sampling to calculate PMF curve for the detachment<br>
> of a terminal cyclic peptide with 8 aa's (CP) from the self-assembled<br>
> cyclic peptide nanotube. I extracted the reaction coordinates staring<br>
> from 5.5 ang COM distance between the terminal CP and the 2nd CP to 17.5<br>
> ang, I did umbrella sampling on 25 configurations (for 5ns) and the<br>
> window size is 0.5 ang. I used the following pulling code for umbrella<br>
> sampling,<br>
><br>
> pull = umbrella<br>
> pull_geometry = distance<br>
> pull_dim = N N Y<br>
> pull_start = yes<br>
> pull_ngroups = 1<br>
> pull_group0 = Chain_B<br>
> pull_group1 = Chain_A<br>
> pull_init1 = 0<br>
> pull_rate1 = 0.0<br>
> pull_k1 = 1000<br>
> pull_nstxout = 1000<br>
> pull_nstfout = 1000<br>
><br>
><br>
> I restrained the 2nd CP unit and the pull_rate1 is 0, so the COM<br>
> distance between the chain_A (terminal) and chain_B (2nd CP) should be<br>
> restrained. after 5ns of umbrella sampling, I calculated the COM<br>
> distance between chain A and B, but it was not restrained, for the 5.5<br>
> ang COM distance restrain, the COM distance varies from 4.5 to 5.5 ang.<br>
> and also the pulling cyclic peptide undergoes large conformational<br>
> sampling. from the WHAM analysis I understood the sampling window is<br>
> poorly represented. In addition to COM distance restrain, can I restrain<br>
> the pulling CP's backbone atoms? so that the pulling groups large<br>
> conformational sampling will be reduced.<br>
<br>
You could implement dihedral restraints to fix the backbone secondary structure,<br>
but I can't comment on the stability of trying to use these restraints in<br>
addition to the pull code. Seems like a lot going on at once, to me.<br>
<br>
Also consider the fact that 5 ns is an extremely short timeframe to gather<br>
meaningful data. Perhaps you just need more time in each window to equilibrate.<br>
At the shortest COM distance, your two molecules are still likely experiencing<br>
some interactions, and it may require a great deal of sampling in this window to<br>
converge the simulations. You haven't shown the rest of your .mdp file (always<br>
a good idea!), so we can only guess at whether or not your other settings should<br>
lead to a sensible result.<br>
<br>
-Justin<br>
<br>
--<br>
========================================<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> | (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>
<br>
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<br>
<br>
</blockquote></div><br></div>