[gmx-users] PMF in vacuum and pull direction

chris.neale at utoronto.ca chris.neale at utoronto.ca
Tue Jun 8 14:05:23 CEST 2010

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.


-- 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
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

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Today's Topics:

    1. Constraint causing system to explode (Warren Gallin)
    2. PMF in vacuum (chris.neale at utoronto.ca)
    3. Re: Compile gromacs 4.0.7 with mopac (Stefan Hoorman)
    4. vibrational spectra of glucose (Nilesh Dhumal)


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";

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

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.


-- 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.


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

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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