[gmx-users] Re: g_wham problem with negative COM differences
Thomas Schlesier
schlesi at uni-mainz.de
Wed Apr 18 14:38:54 CEST 2012
Am 18.04.2012 12:00, schrieb gmx-users-request at gromacs.org:
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> Today's Topics:
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> 1. Re: g_wham problem with negative COM differences (Anni Kauko)
> 2. Error- Atom not found in residue seq nr while adding atom
> (aiswarya pawar)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 18 Apr 2012 12:19:08 +0300
> From: Anni Kauko<akauko at sbc.su.se>
> Subject: Re: [gmx-users] g_wham problem with negative COM differences
> To: gmx-users at gromacs.org
> Message-ID:
> <CALxANdPFxZgYhxdVbsqMSrfgY7-MaN2F_-VDkbpkrgtZQ-tYUw at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
>> Anni Kauko wrote:
>>>>
>>>> Date: Wed, 11 Apr 2012 08:38:05 -0400
>>>> From: "Justin A. Lemkul"<jalemkul at vt.edu<mailto:jalemkul at vt.edu
>>>>
>>>> Subject: Re: [gmx-users] g_wham problem with negative COM
>> differences
>>>> To: Discussion list for GROMACS users<gmx-users at gromacs.org
>>>> <mailto:gmx-users at gromacs.org>>
>>>> Message-ID:<4F857B2D.3050100 at vt.edu
>> <mailto:4F857B2D.3050100 at vt.edu>>
>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>>>
>>>>
>>>>
>>>> Anni Kauko wrote:
>>>> > Hi!
>>>> >
>>>> > I try to perform pmf calculations for case where a peptide
>> shifts
>>>> > through the membrane. My COM differences should vary from 2.3 to
>>>> -2.5.
>>>> >
>>>> > My problem is that g_wham plots negative COM difference as they
>>>> would be
>>>> > positive. In pullx-files the COM differences are treated
>> correctly
>>>> > (look below). My peptide is not symmetric, so profile curves
>> are not
>>>> > symmetric, so loosing the sign for COM difference screws my
>> profile
>>>> > curve completely.
>>>> >
>>>> > I did not manage to find any pre-existing answers to this
>> problem
>>>> from
>>>> > internet.
>>>> >
>>>> > First datalines from pullx files:
>>>> > (sorry for strange file names...)
>>>> >
>>>> > pull_umbr_0.xvg:
>>>> > 0.0000 6.26031 2.27369
>>>> >
>>>> > pullz_umbr_23.xvg:
>>>> > 0.0000 6.09702 0.0233141
>>>> >
>>>> > pullz_umbr_50.xvg:
>>>> > 0.0000 6.02097 -2.50088
>>>> >
>>>> > g_wham command:
>>>> > g_wham -b 5000 -it tpr_files.dat -ix pullz_files.dat -o
>>>> > profile_test.xvg -hist histo_test.xvg -unit kCal
>>>> >
>>>> > My pull code:
>>>> >
>>>> > pull = umbrella
>>>> > pull_geometry = distance
>>>> > pull_dim = N N Y
>>>> > pull_start = yes
>>>> > pull_ngroups = 1
>>>> > pull_group0 = POPC_POPS ; reference group is bilayer
>>>> > pull_group1 = C-alpha_&_r_92-94 ; group that is actually
>> pulled
>>>> > pull_init1 = 0
>>>> > pull_rate1 = 0.0
>>>> > pull_k1 = 1000 ; kJ mol-1 nm-2
>>>> >
>>>>
>>>> Your problem stems from the use of "distance" geometry. This
>> method
>>>> assumes the
>>>> sign along the reaction coordinate does not change, i.e. always
>>>> positive or
>>>> always negative. If the sign changes, this simple method fails.
>>>> You should be
>>>> using something like "position" to allow for a vector to be
>>>> specified. Perhaps
>>>> you can reconstruct the PMF by separately analyzing the positive
>>>> restraint
>>>> distances and negative restraint distances (note here that
>>>> "distance" really
>>>> refers to a vector quantity, and thus it can have a sign), or
>>>> otherwise create
>>>> new .tpr files using "position" geometry, though I don't know if
>>>> g_wham will
>>>> accept them or not.
>>>>
>>>> -Justin
>>>>
>>>> --
>>>> ========================================
>>>>
>>>> Justin A. Lemkul
>>>> Ph.D. Candidate
>>>> ICTAS Doctoral Scholar
>>>> MILES-IGERT Trainee
>>>> Department of Biochemistry
>>>> Virginia Tech
>>>> Blacksburg, VA
>>>> jalemkul[at]vt.edu<http://vt.edu> | (540) 231-9080
>>>> <tel:%28540%29%20231-9080>
>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>
>>>> ========================================
>>>>
>>>>
>>>> Thank's!
>>>>
>>>> I managed to solve my g_wham problem by doing two things:
>>>>
>>>> 1. New tpr-files with proper pull code for g_wham.
>>>> 2. I also needed to modify signs of pullf values: If value for pullx
>>>> distance was negative, I reversed the sign of corresponding pullf
>> value.
>>>> I did that by my own script.
>>>>
>>>> The new pull code:
>>>>
>>>> ; Pull code
>>>>
>>>> pull = umbrella
>>>> pull_geometry = direction
>>>> pull_vec1 = 0 0 1
>>>> pull_start = yes
>>>> pull_ngroups = 1
>>>> pull_group0 = POPC_POPS ; reference group is bilayer
>>>> pull_group1 = C-alpha_&_r_92-94 ; group that is actually pulled
>>>> pull_init1 = 0
>>>> pull_rate1 = 0.0
>>>> pull_k1 = 1000 ; kJ mol-1 nm-2
>>>>
>>>> I am little bit confuced, why I needed to tweak signes of pullf
>> values.
>>>> But like that I got the curve that resembles two half curve made for
>>>> positive and negative pullx distances separately. That curve also
>> makes
>>>> sense from biochemical point of view.
>>>>
>>> Such changes do not seem appropriate to me. If you change the sign of
>>> the
>>> pulling force, you change the implication of what that value means.
>>> What
>>> happens if you run your simulations with the new (more appropriate)
>>> .mdp file?
>>> Do the forces have the same magnitude, but opposite sign?
>>
>> I don't think that the problem is so easy fixed. I had with another
>> person about a month ago a lengthy discussion on the list.
>>
>> The problem is the following:
>> If you use 'distance' as pull_geometry the position of the minimum of
>> the umbrella potential is determined by the vector connecting the ref-
>> and pulled group, but there is no information about the direction.
>>
>> Assume this (1D):
>> reference particle at origin (0)
>> minimum of umbrella potential (1) - via pull_init1 = 1
>> pulled particle at (0.5)
>> -> force acting of pulled particle 0.5*k
>> -> everything ok
>> --------------------------------------------------------
>> we look later and pulled particle moved to (-0.5)
>> since we are in the same umbrella sampling windows the umbrella
>> potential minimum should still be at (1) -> force acting would be 1.5*k
>> (this would be right if we had direction as the pull_geometry)
>> BUT:
>> we have pull_geometry=distance
>> -> minimum of umbrella potential is now at (-1)
>> (why is this: from ref seen pull-group is now in the negative direction
>> -> pull_init tells use that we should go along this vector the distance
>> 1 -> new position is now (-1))
>> -> force acting is now -0.5*k
>> which is wrong (meaning physical not sensible)
>> ok, the force is right (from the algorithm standpoint), but the fact
>> that our minimum of the umbrella potential jumps around during the
>> sampling screws everything
>> --------------------------------------------------------------
>>
>> hope you get the idea about the origin of problem
>>
>> greetings
>> thomas
>>
>>
> It seems that it is safest if I simply rerun my all simulations... Then we
> will see how it really is.
>
> I'm not sure if I understand correctly, but doesn't Thomas's experience
> also suggest that for some strange algoritmic reason force get's wrong sign
> when distance gets negative with distance geometry? Or am I completely
> confuced? If it is so, wouldn't my trick then be justified?
>
> At least if I plot two half curves separately for positive and negative
> distances (I discarded all runs around zero), I get results that are
> compatible with my sign trick. And It also made sense biochemically. But
> well, proper rerun does not leave any questions.
>
> Does following pull code seem proper to you:
>
>
> pull = umbrella
> pull_geometry = direction
> pull_vec1 = 0 0 1
> pull_start = yes
> pull_ngroups = 1
> pull_group0 = POPC_POPS ; reference group is bilayer
> pull_group1 = C-alpha_&_r_92-94 ; group that is actually pulled
> pull_init1 = 0
> pull_rate1 = 0.0
> pull_k1 = 1000 ; kJ mol-1 nm-2
>
>
> Regards,
> Anni
>
It's not really 'strange algoritmic reason', more an algorithmic
problem. One could say it so: For 'pull_geometry=distance' the problem
is isotropic, you pull along the vector connecting the two groups. If
the two groups switch places -> the direction of the vector changes ->
origin of potential jumps
With 'pull_geometry=direction' you pull along a defined vector. If both
groups switch places -> but still vector stays the same -> origin of
potential stays where it was
So in theory 'pull_geometry=direction' should solve the problem with
umbrella sampling a really small distances,
*BUT* as far as i know 'g_wham' doesn't like 'pull_geometry=direction'.
One idea (but absolut no idea if i will work):
Run the problematic windows/distances with 'pull_geometry=direction' and
make a *.tpr file with 'pull_geometry=distance' and just feed this to
g_wham. One thing which is important is the 'pull_dim'. If it is 1D you
are fine. If it is 3D, you must calculate the absolute of each force and
give it the 'right' sign.
One thing to note:
I think to problem occurs only for a handfull of umbrella-sampling
windows around a distance of 0. And even there, for the larger (but
still relative small) distances it becomes less problematic (since the
switching of both groups happens less often).
Greetings
Thomas
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