Den 2020-03-29 kl. 22:46, skrev Alex:
On Sun, Mar 29, 2020 at 2:49 PM David van der Spoel <sp...@xray.bmc.uu.se>
wrote:
Den 2020-03-29 kl. 19:43, skrev Alex:
Thanks.
On Sun, Mar 29, 2020 at 11:59 AM David van der Spoel <
sp...@xray.bmc.uu.se>
wrote:
Den 2020-03-29 kl. 15:16, skrev Alex:
Thank Prof. van der Spoel for the response.
No, it isn't. The thin film is solid. There are interaction within the
thin
film and with water in the interface.
Please find a short movie of the unwrapped trajectory of the simulation
in
below link (water molecules are hidden); It shows minimization, then
equalization (NVT : tcoupl = v-rescale), then equalization (NpT :
tcoupl
=
v-rescale and pcoupl = berendsen) and then production (NpT : tcoupl =
v-rescale and pcoupl = Parrinello-Rahman).
https://drive.google.com/open?id=1jk-Pun1BICNArGJaW0ydIY5TTivECGMf
The thin film starts drifting significantly in the production along
both
x
and y directions.
Thanks, do you have isotropic pressure scaling?
Yes, the pcoupltype is isotropic. Please find the mdp file in below link.
https://drive.google.com/open?id=1iYt6eTcQ4SBi1A9ZFOenL7Q7wc37UvLa
Is the shift towards higher x and y values?
The shift is toward higher y value (+y).
It also firstly goes toward higher x value (+x ) for a very short time
and
then switches the direction to toward lower x value (-x) and finally
shifts
toward lower x value (-x).
But how is the solid modeled? Are there covalent bonds? It is not
certain there is a problem, at least I am not convinced. In P scaling
the coordinates of all particles are scaled by a constant and then
certain atoms can hop over PBC. If you plot the center of mass including
periodic boundaries (i.e. without unwrapping) it will be nicely in the
center of the box with few fluctuations. gmx traj may do this for you.
The thin film contains 1075 epoxy molecules in which there is no
inter-molecule covalent bond.
Below are the COM of the thin film with and without pbc in gmx traj.
I admit you are right and the comm-grps works fine as gmx traj -pbc yes
shows, thanks.
PBC : Yes
https://drive.google.com/open?id=14DRIZVt99x8SfO6qlkhPAeTkb7RQhsUp
PBC: No
https://drive.google.com/open?id=1uWRgTATW9hUEOaQQnQozklUvux8psrPx
Note that the net movement is a lot smaller than the fluctuations in the
in the one with PBC, I don't think there is any problem.
I and many others have done PMFs of small compounds over membranes of
different types, but not sure that anyone has noticed problems with
moving membranes.
I would also be so appreciated if you give me your preferences of the
following two choices I have in the PMF calculation of Mol_A to the
thin-film.
“comm-grps = *thin_film* *Mol_A* *SOL*”
or
“comm-grps = *Other* *SOL*”
Where the Other group contains the thin film and molecule A.
I would go for comm-grps = system.
Make sure to compute the pmf based on the relative distance between your
compound and the membrane.
Best regards,
Alex
Maybe you can open an issue here:
https://gitlab.com/gromacs/gromacs/-/issues
I will open an issue.
Actually, in the later steps of the simulations, using umbrella sampling
and wham, I want to simulate the PMF a single molecule (called A; 26
atoms)
when it comes from water and diffuses inside the thin film till mid (com)
of thin film. pull_group1 and pull_group2 would be the Mol_A and
thin_film,
respectively.
I don't know if this kind of drifting would affect on the PMF, if so,
how?
If the comm-grps works I have the two following options to consider:
“comm-grps = thin_film Mol_A SOL”
or
“comm-grps = Other SOL”
Where the Other group contains the thin film and molecule A.
Which one do you recommend, please?
Thank you,
Alex
Best regards,
Alex
On Sun, Mar 29, 2020 at 2:44 AM David van der Spoel <
sp...@xray.bmc.uu.se>
wrote:
Den 2020-03-29 kl. 05:24, skrev Alex:
Dear all,
In a system, I have a thin_film (infinitive in x-y directions) with
water
on top and bottom of it, PBC = xyz.
By the below flags I try to remove the motion of the center of mass
of
the
two group separately.
comm-grps = thin_film Water
comm-mode = Linear
nstcomm = 100
However the thin film drift specially in x and y directions whereas I
was
expecting to have no drifting for the thin film, If I understood
correctly
the usage of the comm-grps!
Would you please let me know how I can stop drifting of the thin
film?
Thank you,
Alex
Is that a liquid film? Are there interactions within the film and with
water? The comm removal will calculate the center of mass taking
periodic boundaries into account so if your film moves one molecule
at a
time the COM will stay in place. In a realistic system the friction
between water and film should prevent this, hav eyou tried turning off
comm?
Historically this has been a fix for the Berendsen thermostat that
accumulates energy, however with a stochastic thermostat it should not
be necessary. Not sure about Nose-Hoover though.
--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
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Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
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--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
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--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
--
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