[gmx-users] PMF in vacuum and pull direction (chris.neale at utoronto.ca)
Eudes Fileti
fileti at ufabc.edu.br
Tue Jun 8 19:02:26 CEST 2010
Hello Chris, thanks for the reply. Below his message commented walkthrough.
In your email you asked me for quantitative results. All I have so far is
a visual inspection of the pulling trajectory. All I can see are
the two molecules moving linearly away from each other in a rectangular box
of dimensions 3x3x6nm. However this separation does not occur on the z
axis,
as I wanted, but in a diagonal way across the faces of the box.
Bests
eef
> 1. There is no need to use a virtual atom, the pull code will use the
> center of mass. I strongly suggest that you stop using a virtual atom
> and just use the entire benzene as an argument to the pull code group.
> I have had difficulties with slightly more complicated setups of this
> type.
Ok, now I'm using only the center of mass of the molecules, no virtual
sites.
> 2. In test2.jpg, the system without pbc shows a flat PMF after the
> cut-off -- exactly what one would expect. The pbc system shows
> continued interaction -- again what I would expect. So there is
> nothing actually all that strange here. One would not expect to see
> such a drastic difference in a high dielectric such as water, but in
> vacuum I suspect that this is expected.
Alright! In fact the well of both PMFs are not so different.
> 3. Please clarify what your cutoff was. I don't see a cut-off listed
> in your .mdp options and leaving this to the default of 1.0 nm is a
> bad idea because it can lead to confusion a times like this. I might
> assume that it was 0.7 nm based on test2.jpg, but then see the point
> #3 below.
Apesar de eu nao ter incluido o valor do cutoff na mensagem anterior
eu usei 1.2 nm
Although I have not included the cutoff value in previous message
I used it as 1.2 nm.
> 4a. I have no idea what -DPOSRES is actually doing for you since I
> can't see your topology.
A ideia de usar POSRES se referia ao emprego dos sitios virtuais.
Assim eu restringia a distancia das moleculas atraves da restricao do
sitios virtuais sobre seus centros.
The idea of using POSRES is referred to the employment of the virtual sites.
So I restricted the distance of molecules by restricting virtual sites
on their centers.
>
> 4b. Are you sure that "pull_dim = N N Y" is really what you want?
> Sometimes one wants to average over X and Y, but I am not sure that
> you do in this case.
I want to separate the two molecules from one another so that the
displacement is restricted to the z axis. I can be wrong,
but I think to do it in water, using PBC, I should use the
components distance (N N Y ) with direction geometry to get a
pulling in a direction z! Please correct me if it is wrong.
> 4c. What exactly do you believe pull_r0 and pull_r1 are doing for you?
Here they are worthless, because I have not used the option "cylinder".
I should have removed these options from the original message.
> ### More minor notes:
>
> 5. regarding test1.jpg: a PMF is correct to an additive constant,
> meaning that you can shift two PMFs relative to one another. These 2
> PMFs are therefore less different than they appear in your compaison
> plot, but they do differ in the slope between 1.0 - 2.0 nm. This is
> probably just a convergence issue and you will always need to do tests
> like this.
Surely.
> 6. regarding histo.png: can you confirm that the few very short
> gaussians are due to less sampling in a few windows? In any event, the
> overlap looks good.
Yes, there were two histograms whose simulations had crashed for some
reason.
It was corrected.
_______________________________________
Eudes Eterno Fileti
Centro de Ciências Naturais e Humanas
Universidade Federal do ABC — CCNH
Av. dos Estados, 5001
Santo André - SP - Brasil
CEP 09210-971
+55.11.4996-0196
http://fileti.ufabc.edu.br
4. PMF in vacuum and pull direction (chris.neale at utoronto.ca)
>
>
>
> Message: 4
> Date: Tue, 08 Jun 2010 12:14:34 -0400
> From: chris.neale at utoronto.ca
> Subject: [gmx-users] PMF in vacuum and pull direction
> To: gmx-users at gromacs.org
> Message-ID: <20100608121434.u6rhqhz400gc8cg8 at webmail.utoronto.ca>
> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
> format="flowed"
>
> Dear Eudes:
>
> This is better, but I'm afraid that I'm going to have to insist on
> getting everything I asked for. Please see my previous message.
>
> Chris.
>
> -- original message --
>
> Dear Chris, I'm so sorry for surperficial email.
> You are correct because in the previous message
> I forgot to mention that now the simulation was
> performed in water (naturally with PBC).
> The main parameters of the simulation are given below.
> As I said, I wish to keep the displacement of the pulled molecule at
> the z-axis, but I'm not getting with this protocol.
>
> For the vacuum I followed the tips you gave me earlier and had success!
> Thanks
> eef
>
>
>
> title = Umbrella pulling simulation
> integrator = sd
> dt = 0.002
> nsteps = 3000000
> constraint_algorithm = lincs
> constraints = all-bonds
> nstlist = 5
> ns_type = simple
> rlist = 1.2
> rcoulomb = 1.2
> rvdw = 1.2
> coulombtype = Cut-off
> Tcoupl = V-rescale
> tc_grps = system
> tau_t = 0.1
> ref_t = 298
> Pcoupl = no
> pcoupltype = isotropic
> tau_p = 1.0
> compressibility = 4.5e-5
> ref_p = 1.0
> pbc = xyz
>
> ; Pull code
> pull = umbrella
> pull_geometry = direction
> pull_dim = N N Y
> pull_start = yes
> pull_ngroups = 1
> pull_group0 = BEN1
> pull_group1 = BEN2
> pull_vec1 = 0 0 1
> pull_rate1 = 0.001
> pull_k1 = 1600
>
>
>
> > Message: 4
> > Date: Tue, 08 Jun 2010 08:05:23 -0400
> > From: chris.neale at utoronto.ca
> > Subject: [gmx-users] PMF in vacuum and pull direction
> > To: gmx-users at gromacs.org
> > Message-ID: <20100608080523.i6oo62he1wwc0wkg at webmail.utoronto.ca>
> > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
> > format="flowed"
> >
> > Dear Eudes:
> >
> > You can make my job a whole lot easier! First, please go back through
> > all of the comments that I gave you last time and reply to them one by
> > one. Did you do them? What did you see? Second, please include your
> > new .mdp and some quantitative results to better explain what you see
> > (e.g. your .px file and a description of why the values are not what
> > you expect).
> >
> > Sorry if this sounds annoying, but there's no point in my working in the
> > dark.
> >
> > Chris.
> >
> > -- original message --
> >
> > Hello Chris, thanks for the tips, they were very helpful.
> > Now a new problem appeared. I'm trying to separate the
> > two benzene molecules from one another while maintaining
> > the displacement vector aligned with the z axis. For that I
> > have used "pull_geometry = direction". However, at the end of the
> > simulation, I notice that the desired alignment (with z) was
> > not maintained. The molecule is pulled away from z and eventually
> > crosses the PBC. I took a good look at gmx-list and noticed
> > that you rode conducting tests with this option. Could you give
> > me a light on this problem too? Grateful
> > eef
> > _______________________________________
> > Eudes Eterno Fileti
> > Centro de Ciências Naturais e Humanas
> > Universidade Federal do ABC ? CCNH
> > Av. dos Estados, 5001
> > Santo André - SP - Brasil
> > CEP 09210-971
> > +55.11.4996-0196
> > http://fileti.ufabc.edu.br
> >
> >
> > Message: 2
> > Date: Thu, 27 May 2010 12:12:03 -0400
> > From: chris.neale at utoronto.ca
> > Subject: [gmx-users] PMF in vacuum
> > To: gmx-users at gromacs.org
> > Message-ID: <20100527121203.orb2sq228s4ow0wg at webmail.utoronto.ca>
> > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
> > format="flowed"
> >
> > Dear Eudes:
> > To answer your pbc vs no-pbc question, I suggest that you use pbc=no
> > and set nstlist=0 rlist=0 rvdw=0 rcoulomb=0 so that you calculate all
> > interactions in direct space with no cutoffs.
> >
> > ## Major comments that you should still investigate
> >
> > 1. There is no need to use a virtual atom, the pull code will use the
> > center of mass. I strongly suggest that you stop using a virtual atom
> > and just use the entire benzene as an argument to the pull code group.
> > I have had difficulties with slightly more complicated setups of this
> > type.
> >
> > 2. In test2.jpg, the system without pbc shows a flat PMF after the
> > cut-off -- exactly what one would expect. The pbc system shows
> > continued interaction -- again what I would expect. So there is
> > nothing actually all that strange here. One would not expect to see
> > such a drastic difference in a high dielectric such as water, but in
> > vacuum I suspect that this is expected.
> >
> > 3. Please clarify what your cutoff was. I don't see a cut-off listed
> > in your .mdp options and leaving this to the default of 1.0 nm is a
> > bad idea because it can lead to confusion a times like this. I might
> > assume that it was 0.7 nm based on test2.jpg, but then see the point
> > #3 below.
> >
> > 4a. I have no idea what -DPOSRES is actually doing for you since I
> > can't see your topology.
> >
> > 4b. Are you sure that "pull_dim = N N Y" is really what you want?
> > Sometimes one wants to average over X and Y, but I am not sure that
> > you do in this case.
> >
> > 4c. What exactly do you believe pull_r0 and pull_r1 are doing for you?
> >
> > ### More minor notes:
> >
> > 5. regarding test1.jpg: a PMF is correct to an additive constant,
> > meaning that you can shift two PMFs relative to one another. These 2
> > PMFs are therefore less different than they appear in your compaison
> > plot, but they do differ in the slope between 1.0 - 2.0 nm. This is
> > probably just a convergence issue and you will always need to do tests
> > like this.
> >
> > 6. regarding histo.png: can you confirm that the few very short
> > gaussians are due to less sampling in a few windows? In any event, the
> > overlap looks good.
> >
> > Chris
> >
> > -- original message --
> >
> > Hello Chris, thanks for your attention.
> > I'm sending you some links to some tests
> > I performed. As I said you will notice that
> > depending on the parameter used my simulation
> > shows PMF profiles quite different. Especially what
> > concerns to the difference between the use or not of the PBC.
> >
> > https://sites.google.com/site/fileti/files/test1.jpg
> > https://sites.google.com/site/fileti/files/test2.jpg
> > https://sites.google.com/site/fileti/files/histo.png
> >
> > I have constructed two very similar topologies (ben-a.itp and ben-b.itp)
> > where I put a virtual site in the center of benzene.
> > This sites were restrained to keep my molecules
> > fixed distance desired.
> >
> > The basic details of the simulations are given below:1000
> >
> > define = -DPOSRES
> > integrator = sd
> > tinit = 0
> > dt = 0.002
> > nsteps = 5000000 or 500000
> > comm-mode = angular
> > nstcomm = 1
> > comm-grps = System
> > bd-fric = 1
> > ld-seed = 1993
> > nstlist = 5
> > ns_type = simple
> > pbc = no or xyz
> > periodic_molecules = no
> > rlist = 0
> > coulombtype = Cut-off
> > vdw-type = Cut-off
> > rvdw = 0
> > DispCorr = no
> > Tcoupl = Nose-Hoover
> > tc_grps = system
> > tau_t = 0.1
> > ref_t = 300
> > Pcoupl = no
> > pcoupltype = isotropic
> > tau_p = 1.0
> > compressibility = 4.5e-5
> > ref_p = 1.0
> > constraints = all-bonds
> > constraint_algorithm = lincs
> >
> > ; COM PULLING
> > pull = umbrella
> > pull_geometry = distance
> > pull_dim = N N Y
> > pull_r1 = 1
> > pull_r0 = 1.5
> > pull_constr_tol = 1e-06
> > pull_start = yes
> > pull_nstxout = 10
> > pull_nstfout = 10
> > pull_ngroups = 1
> > pull_group0 = BENa
> > pull_weights0 =
> > pull_pbcatom0 = 0
> > pull_group1 = BENb
> > pull_weights1 =
> > pull_pbcatom1 = 0
> > pull_vec1 = 0 0 1
> > pull_init1 = 0
> > pull_rate1 = 0.0
> > pull_k1 = 1700 or
> >
> >
> >
>
>
>
>
> ------------------------------
>
> --
> gmx-users mailing list
> gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
>
> End of gmx-users Digest, Vol 74, Issue 53
> *****************************************
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100608/530f652b/attachment.html>
More information about the gromacs.org_gmx-users
mailing list