[gmx-users] PMF in vacuum and pull direction (chris.neale at utoronto.ca)
Eudes Fileti
fileti at ufabc.edu.br
Tue Jun 8 16:44:26 CEST 2010
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
>
>
>
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