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Yep, my case is b :(... Gromacs do writes pullx as ref COM global coords and pull COM displacement. And I still don't realize what is force value in pullf but it gives identical results for both -if and -ix options of g_wham. And g_wham do works OK at least for 2 waters separation in 0.3-1nm scale... probably my run should produce snaps more frequently, say each ps... will try this.
<br />Regards,
<br />Alex
<br />
<br />
<blockquote class="ukr_editor_quotation" style="border-left: 1px solid rgb(204, 204, 204); margin: 0px 0px 0px 0.8ex; padding-left: 1ex;">Sorry Alex, but there is no good substitute what I have already
<br />suggested. I helped you find a lead and I suggested a way to simplify
<br />your system to discover what is going on. Now it's up to you to do
<br />that work.
<br />
<br />It might end up being a bug, but I doubt it. I have done things
<br />similar to what you are doing and have no problems. And even if it is
<br />a bug, then the developers will need you to find a simple version of
<br />the problem in any event.
<br />
<br />Make the water box, pull two waters, try to match up the force and
<br />energy values from your pull output files.
<br />
<br />Note that you have forgotten the 1/2 factor in your energy function so
<br />there is no factor of 2 in your force. Also, the force is the negative
<br />derivative. Check the manual for the exact equations.
<br />
<br />Chris.
<br />
<br />Quoting alexander yakovenko <yakovenko_a@ukr.net>:
<br />
<br />> It is 2 options why I can’t understand relation between pullf and
<br />> pullx: either I have no imagine how they should related or they
<br />> related so that one can’t even imagine (say due to bug or file
<br />> format). Till now my view was that we need a force to keep two
<br />> molecules at asked separation. The force is F=2*k*x (or 2*k*|r| in
<br />> case of Y Y Y) and work spent on this is k*x^2. Thus in pullx we
<br />> have either a) coordinates of COMs of both groups or b) COM of
<br />> reference group and relative displacement of pulling group and in
<br />> pullf we have 2*k*x values. The problem is that I can’t substitute
<br />> data from pullx so to get data from pullf and thus I don’t realize
<br />> these relations. Say pullx line is 11984.0000
<br />>
<br />> 3.12086 4.37951 -1.63297 1.98567 2.64212
<br />> -3.25943 so |r| is a) 4.641936 if dx, dy and dz are displacements
<br />> or b) 2.63676933 if dx, dy and dz are just coordinates of
<br />> pulling group COM. Suggesting |ro| to be 2.383+1.0=3.383 nm
<br />> (equilibrated complex position + displacement of 1.0 nm) and k=1000
<br />> kJ/mol/nm^2 we have force of a) 9283.871 or b)
<br />> 5273.53865 kJ/mol/nm. Unfortunately neither of these values
<br />> looks like 332.586 from pullf file... So can you please help
<br />> me to choose my option: a) mdrun is corrupted, b) I don’t
<br />> understand what I am doing or c) pullf and pullx writes some
<br />> specific format of output that should be processed by g_wham to
<br />> make some sense? Because if it is a) I have to post bugzilla, if b)
<br />> I have to deal with water, if c) I have to post gromacs-users in
<br />> order to launch g_wham.
<br />>
<br />> Regards,
<br />>
<br />> Alex
<br />>
<br />> >
<br />>
<br />> >
<br />>
<br />> So now we have the first real lead. Next is for you to simplify your
<br />> system to the point where you *can* understand the relationship
<br />> between the pullf and pullx files. For example, I always suggest a
<br />> water bath of explicit water with the sd integrator and apply the pull
<br />> code to two waters.
<br />>
<br />> It's time for you to bash your head against this one on your own until
<br />> you can find a simple system that has no problem and then a slightly
<br />> more complex system that has the problem. Bring those back to the list
<br />> and we can help again if you can;t figure it out.
<br />>
<br />> PS: you should file a bugzilla or otherwise try to get the gromacs
<br />> list fixed so that you can post directly.
<br />>
<br />> Chris.
<br />>
<br />> Quoting alexander yakovenko < yakovenko_a@ukr.net >:
<br />>
<br />> > Sorry for mixing things, I do pull into N Y N direction and then
<br />> > performed umbrella simulation at Y Y Y for each distances window.
<br />> > This is very good question, actually I don't realize it too. The only
<br />> > thing what I can say is that I haven't edited/renamed these files,
<br />> > just copy them. So this is pure output of mdrun, hopes it knows what
<br />> > it writes... I can provide a tpr of a window for example so you can
<br />> > check couple first strings (for reproduction, I carried out all
<br />> > calculations on 8x Xeons@2.66 workstations).
<br />> > Alex
<br />> > >
<br /></blockquote>
<br />
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