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<div>I dont know how well v-rescale works with pulling. It could be after removing some restraints it still had not reached a good equilibrium (ie let it run a while/nanosecound or 5, before pulling it), or maybe generating velocities on start causes more caos than the proteins or system can handle, still it may be the real system minus several initial time frames, ie it either isnt bound from the start as it is in reality or it prefers to be free...But I may be wrong on some of this...so just suggestions. Also, 500 picoseconds is short for measring things, and would probably be dominated by starting velocity for at least 40-80 picoseconds, thus look at how fast it declines...there are some printed standards for protein-protein delG or domain changes of around 3-4 ns to make sure small loop/domain changes are represented in the energy profile. There was (on some comments) talk of making this around 6 ns..but I dont know if there are set real standards for this held fast to (i've read 2 papers with 400 ns to see domain changes with no pull, and a good 5-6 at 4 ns with pulling so?).</div>
<div> </div>
<div>Stephan Wakins</div>
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<div style="margin:0 0 10px 0;"><b>Gesendet:</b> Dienstag, 29. Oktober 2013 um 20:27 Uhr<br/>
<b>Von:</b> "XAvier Periole" <x.periole@rug.nl><br/>
<b>An:</b> "Discussion list for GROMACS users" <gmx-users@gromacs.org><br/>
<b>Betreff:</b> Re: [gmx-users] Constant-Force Pulling of Ubiquitin</div>
<div name="quoted-content"><br/>
You want to switch to sd instead of md.<br/>
<br/>
> On Oct 29, 2013, at 17:43, Vivian <wwtao@bu.edu> wrote:<br/>
><br/>
> Hi GMX Users,<br/>
><br/>
> I am using Gromacs (Version 4.5.5) to do constant-force pulling of ubiquitin<br/>
> and it's a implicit model. My mdp file for pulling is shown as following.<br/>
><br/>
> integrator = md<br/>
> dt = 0.001 ; ps !<br/>
> nsteps = 500000 ; total 500 ps.<br/>
><br/>
> nstxout = 100<br/>
> nstvout = 100<br/>
> nstfout = 100<br/>
> nstlist = 10<br/>
> nstlog = 100<br/>
> nstcalcenergy =100<br/>
><br/>
> rlist = 5<br/>
> rvdw = 5<br/>
> rcoulomb = 5<br/>
> coulombtype = cut-off<br/>
> vdwtype = cut-off<br/>
> table-extension = 5<br/>
> bd_fric = 0<br/>
> ld_seed = -1<br/>
> pbc = no<br/>
> ns_type = simple<br/>
> constraints = all-bonds<br/>
> lincs_order = 4<br/>
> lincs_iter = 1<br/>
> lincs-warnangle = 30<br/>
><br/>
> Tcoupl = v-rescale<br/>
> tau_t = 1.0<br/>
> tc-grps = Protein<br/>
> ref_t = 300<br/>
><br/>
> Pcoupl = no<br/>
><br/>
> gen_vel = yes<br/>
> gen_temp = 300<br/>
> gen_seed = 173529<br/>
><br/>
> comm_mode = Angular<br/>
> nstcomm =100<br/>
><br/>
><br/>
> ; IMPLICIT SOLVENT ALGORITHM<br/>
> implicit_solvent = gbsa<br/>
><br/>
> ; GENERALIZED BORN ELECTROSTATICS<br/>
> ; Algorithm for calculating Born radii<br/>
> gb_algorithm = Still<br/>
> ; Frequency of calculating the Born radii inside rlist<br/>
> nstgbradii = 1<br/>
> ; Cutoff for Born radii calculation; the contribution from atoms<br/>
> ; between rlist and rgbradii is updated every nstlist steps<br/>
> rgbradii = 5<br/>
> ; Dielectric coefficient of the implicit solvent<br/>
> gb_epsilon_solvent = 80<br/>
> ; Salt concentration in M for Generalized Born models<br/>
> gb_saltconc = 0<br/>
> ; Scaling factors used in the OBC GB model. Default values are OBC(II)<br/>
> gb_obc_alpha = 1<br/>
> gb_obc_beta = 0.8<br/>
> gb_obc_gamma = 4.85<br/>
> gb_dielectric_offset = 0.009<br/>
> sa_algorithm = Ace-approximation<br/>
> ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA<br/>
> ; The value -1 will set default value for Still/HCT/OBC GB-models.<br/>
> sa_surface_tension = 2.05016<br/>
><br/>
> ; Pull code<br/>
> pull = constant_force<br/>
> ;Center of mass pulling using a linear potential and therefore a constant<br/>
> force.<br/>
> pull_geometry = direction<br/>
> pull_start = yes ; define initial COM distance > 0<br/>
> pull_ngroups = 1<br/>
> pull_group1 = Chain_B<br/>
> pull_group0 = Chain_A<br/>
> pull_k1 = -500 ; kJ mol^-1 nm^-2<br/>
> pull_vec1 = 0.0 0.0 1.0<br/>
><br/>
> However, after pulling simulation, it turns out the potential of this system<br/>
> becomes lower rather than higher (from -10000 to -20000). It's very wired<br/>
> since potential should become larger after pulling.<br/>
> Here is the notification after g_energy:<br/>
><br/>
> Energy Average Err.Est. RMSD Tot-Drift<br/>
> -------------------------------------------------------------------------------<br/>
> Potential -20734.5 230 1268.47 -1385.71<br/>
> (kJ/mol)<br/>
><br/>
> You may want to use the -driftcorr flag in order to correct for spurious<br/>
> drift in the graphs. Note that this is not<br/>
> a substitute for proper equilibration and sampling! You should select the<br/>
> temperature in order to obtain fluctuation properties.<br/>
><br/>
> I wonder whether there is any problem with my mdp file.<br/>
> Thank you so much!!<br/>
><br/>
> Best,<br/>
> Vivian<br/>
><br/>
> --<br/>
> View this message in context: <a href="http://gromacs.5086.x6.nabble.com/Constant-Force-Pulling-of-Ubiquitin-tp5012065.html" target="_blank">http://gromacs.5086.x6.nabble.com/Constant-Force-Pulling-of-Ubiquitin-tp5012065.html</a><br/>
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.<br/>
> --<br/>
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