[gmx-users] Re: Wierd results from Umbrella sampling, (Justin A. Lemkul)

Thomas Schlesier schlesi at uni-mainz.de
Tue May 22 18:53:54 CEST 2012

I never worked with the MARTINI (or other coarse-grained) force field, 
but this in the umbrella.mdp

title       = Umbrella pulling simulation
integrator  = md
dt          = 0.019

looks suspicious. The dt is about an order of magnitude greater than one 
uses in normal (bond-)constrainted md-simulations. I know that in 
coarse-grained simulations the potentials are smoother than in atomistic 
force fields and one therefore could use a higher timestep, but i don't 
know if you can go so high.
Anyway you should look for the umbrella potential. If the force constant 
and the timestep are both too high you could get problems:
Assume a particle in a harmonic well. If the force constant is high and 
the timestep too high, you wont sample the harmonic well, but 'jump' 
each time from one side to the other (high force + great timestep -> 
long movement).
So i would test it first with a timestep of 0.002 (same as you used for 
pulling sim).

Am 22.05.2012 18:37, schrieb gmx-users-request at gromacs.org:
> Thank you for your reply, Thomas. Under your explanation, I am well understood of the terms: pull_k and pull_rate.
> Here I upload both md_umbrella.mdp and md_pulling.mdp.
> I have to mention that it is coarse gained system with Martini force field.
> At the same time, i am going to run a simulation without pull code but with LINCS constraint, and also run another system with a huge pull_k but without LINCS. Hope I could get some interesting information.
> With Regards,
> Jiangfeng.
> Message: 3
> Date: Tue, 22 May 2012 16:36:47 +0200
> From: Thomas Schlesier<schlesi at uni-mainz.de>
> Subject: [gmx-users] Re: Wierd results from Umbrella,   sampling (Justin
>          A. Lemkul)
> To:<gmx-users at gromacs.org>
> Message-ID:<4FBBA47F.5010503 at uni-mainz.de>
> Content-Type: text/plain; charset="ISO-8859-1"; format=flowed
> Think it would be best to show the .mdp file, else we can only guess
> what the parameters are.
>   From the histogram it looks like that the force constant of the
> restraining potential is too low, since the histograms are really wide,
> but pull_k1=1000 is a 'normal' value.
> On thing which confueses me is you said that fluctuations from g_dist
> are about 0.4nm, but in the histogram i looks like the distance
> fluctuates about 1nm or even more. for this be sure, that you compare
> the right distances ->  if you pull only in z-direction, the only look
> into the z-direction from the output from g_dist. Since the x, and
> y-directions would be unaffected by the umbrella potential.
> for the error message with the constraints:
> what happens if you run the system with constraints but without the
> pull-code?
> for pull_k1>0 and pull_rate1=0:
> if you're pulling with an umbrella potential pull_k1 defines the force
> constant of the potential (hook'sches law). Let's assume you put a
> spring to your molecule
> with pull_rate1=0, it means that the other end of the spring doesn't
> move, and the spring restrains the position of the molecule (molecule
> cn't diffuse away). in umbrella sampling you want to restrian of
> molecule (or part of it) relative to another one / part ->  so pull_rate1=0
> with pull_rate1>0, it's like you pull the spring away for the molecule,
> spring gets strechted ->  wants to relax ->  molecule follows spring (like
> that what happens in afm pulling)
> Am 22.05.2012 15:40, schriebgmx-users-request at gromacs.org:
>> >  Hi Justin, As for the maximum of 0.4 nm fluctuation of my pulled
>> >  protein, I used g_dist to calculate the distance between my pulled
>> >  protein and stable part in a window, where the distance is treated as
>> >  the fluctuation of the protein along z-axis. Well, from pullx.xvg, the
>> >  position moved a lot (3nm for instance.) As for the windows simulation,
>> >  I didn't apply constraint but only the internal constraint in the itp
>> >  file. I still don't understand why it have to do constraint? why not
>> >  give a fully freedom to run the simulation? In the md_umbrella.mdp, I
>> >  set pull_k1=1000; pull_rate1= 0.0, but apparently, I am confused with
>> >  pull_k1>0 combined with pull_rate1=0. In my mdp, i set "none" to LINCS,
>> >  because if I use "all-bonds", an error of "1099 constraints but degrees
>> >  of freedom is only1074" occurs. Actually, there is no any window with a
>> >  designed distance. Here I attach the histo.xvg, profile.xvg. Thank you
>> >  with regards, Jiangfeng. On 5/22/12 9:36 AM, Du Jiangfeng (BIOCH) wrote:
>>>> >>  >    Dear Justin,
>>>> >>  >
>>>> >>  >    Based on your questions to my simulation, I posted here yesterday hopefully
>>>> >>  >    it was the correct way to reply in this forum.
>>>> >>  >
>> >  You've still replied to the entire digest message (which I've cut out); please
>> >  make sure to keep replies free of superfluous posts in the future.  The archive
>> >  is already pretty hopeless, but let's not make it worse:)
>> >
>>>> >>  >    In this morning I got a list of new windows of umbrella sampling, the overlap
>>>> >>  >    is sufficient enough, but I saw another problem:  In the histogram figure,
>>>> >>  >    the base of peak covers the distance of 2 nm instead of 0.2 nm., that's
>>>> >>  >    horrible! However, when I checked back to the simulation results of each
>>>> >>  >    window, the fluctuation of my pulled protein is only 0.4nm in maximum. So the
>>>> >>  >    base of peak shouldn't cover such long distance, right?
>>>> >>  >
>> >  If the peaks aren't corresponding to the desired restraint distances, then there
>> >  are several potential problems:
>> >
>> >  1. Your restraints aren't set up the way you think they are (check grompp output
>> >  and .tpr file contents to be sure)
>> >  2. Your restraints are ineffectual (in which case you may need to revisit the
>> >  force constant)
>> >
>> >  I can't determine from your description what's going on.  What do you mean by a
>> >  maximum of 0.4 nm fluctuation?  In what quantity?  What do the contents of
>> >  pullx.xvg show you for the problematic window, and for that matter, the others?
>> >      Are any of them producing the desired restraint distances?
>> >
>> >  Again I will ask you to share an image of the histogram and PMF profile; these
>> >  would be very helpful to see.
>> >
>> >  -Justin
>> >
>> >  --
>> >  ========================================

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