[gmx-users] Re: Re[9]: Flat energy profile in g_wham

chris.neale at utoronto.ca chris.neale at utoronto.ca
Tue Aug 31 20:44:11 CEST 2010

Can you post a snip of your pullx and pullf files from the water box  
simulation where you pulled on 2 waters?

Quoting alexander yakovenko <yakovenko_a at ukr.net>:

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

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