On 7/11/17 1:38 PM, Ben Tam wrote:
Hi Justin,
I am trying to get an energy profile when water molecules go through the porous
cage. I am restraint it to z direction because I would like to see the energy
that require to jump from one cage to another. I set up the simulation so that
the structure is repeated at z direction which this will give me more sample
slice for starting configuration. Sorry I am still new to the umbrella sampling.
OK, I see what you're doing now. That should be fine, but without seeing the
histograms it's impossible to know how well things are working. If you're
getting NaN somewhere, that means a gap in the sampling.
-Justin
Best regards,
Ben
________________________________
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul
<jalem...@vt.edu>
Sent: Tuesday, July 11, 2017 18:07
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] umbrella sampling
On 7/11/17 12:53 PM, Ben Tam wrote:
Hi Andre,
Thanks for your answer. Actually I should clarify it is metal-organic-framework
that I am working on which is a porous material. With the k value larger than
100, the histogram become multiple sharp single peak.
Furthermore when I look at individual 0.1nm slides, it runs completely fine
without obvious anomaly. Therefore I am really confused why the profile.xvg
become infinite or "nan".
I'm really confused about your setup. From what it sounds like, your windows
are too narrow to get good sampling, perhaps the force constant is too strong,
and I'm really not sure why you're only applying a restraint along z. What is
the geometry of your system? Don't follow my tutorial too closely, it's not
appropriate for most cases...
-Justin
Best regards,
Ben
________________________________
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of André Farias de
Moura <mo...@ufscar.br>
Sent: Tuesday, July 11, 2017 17:44
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] umbrella sampling
I never did it myself, but generally speaking you don' t expect that there'
s a lot of room inside a crystal for any molecule to diffuse there,
especially when it comes to cross something like a crystallographic plane,
meaning that huge energy barriers should be there, leading to NaN and other
weird numerical issues.
in principle, larger force constants might help you to sample high energy
barrier, but it will be most likely a trial and error procedure until you
fine-tune the forces along the profile.
best
Andre
On Tue, Jul 11, 2017 at 1:09 PM, Ben Tam <btam...@hotmail.co.uk> wrote:
Dear All,
I am doing umbrella sampling for a water molecules moving inside a crystal
structure, however I am running into a problem on the output file with
profile.xvg all value showing “nan”. This error has occurred when I reduce
the slide width from 0.2 nm to 0.1 nm. I have used the exact pull code for
0.2 and 0.1, however only 0.2 has given me meaningful profile. The pull
code I used is the following:
;Pull code
pull = yes
pull_ngroups = 2
pull_ncoords = 1
pull_group1_name = MOL
pull_group2_name = SOL
pull_coord1_type = umbrella ; harmonic biasing force
pull_coord1_geometry = distance ; simple distance increase
;pull_coord1_vec = 0 0 1
pull_coord1_groups = 1 2
pull_coord1_dim = N N Y
pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k = 10 ; kJ mol^-1 nm^-2
pull_coord1_start = yes ; define initial COM distance > 0
and the time step I used is 500 ps, but I have also tried 100 and 50 ps. I
have tried increasing the k value to 50 and 100 with the same results.
The histogram shows many overlap, however when I use k value 100, it is
only giving me individual single peak. Therefore can someone enlighten on
what is going on?
Best regards,
Ben
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Ruth L. Kirschstein NRSA Postdoctoral Fellow
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