flow of water and ions thru a silica pore

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1

Dear Steve
I have see the movie on flow of water and ions thru a silica pore in lammps website. Now my study is similar with it,but I don’t know how to build a model and relevant parameter settings. Could you send the code to me for learning? Tanks vevry much.
Looking forward to your early reply.
Best regards.
Cheng
Central south university of forestry and technology Changsha, China

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2

Dear Steve
I have see the movie on flow of water and ions thru a silica pore in lammps
website. Now my study is similar with it,but I don't know how to build a
model and relevant parameter settings. Could you send the code to me for
learning? Tanks vevry much.

the proper contact person would be paul crozier (as mentioned in the
description of the movie) and before requesting specific inputs, you
should explain your level of expertise in MD in general and LAMMPS in
particular. more inputs used in production simulations are not very
educational and without the proper background knowledge would do more
harm than good. many times it is necessary to build expertise in
stages. that is particularly true for multi-component systems, where
you can get quickly lost in trying to understand the origin of a
particular problem.

axel.

3

Paul is CCd on this email - if he has a script maybe he can send it to you.

Steve

4

Thank you! I have send a e-mail to Paul

5

Thank you! I have send a e-mail to Paul

6

Dear Steve and Axel
I have send an e-mail to Paul, but he has not write back.Paul’s email address is this: pscrozi@…3… ?
And now I have a question. Can I use compass force field in the lammps? Because I use the potential function as follows:![1C3EJP8(OLS8%W88IIKGFX.png|646x141

Can I use the potential function in the lammps?

7

Dear Steve and Axel
I have send an e-mail to Paul, but he has not write back.Paul’s email address is this: pscrozi@…3… ?
And now I have a question. Can I use compass force field in the lammps? Because I use the potential function as follows:![1C3EJP8(OLS8%W88IIKGFX.png|646x141

Can I use the potential function in the lammps?

8

See the class2 package and all the various bond, angle, dihedral, etc styles.

Steve

![1C3EJP8(OLS8%W88IIKGFX.png|646x141

9

I’m attaching some scripts for modeling the flow of water and ions thru a silica pore, but they are quite dated and come with no guarantees or support, so users please beware.

Paul

![1C3EJP8(OLS8%W88IIKGFX.png|646x141

6x6x6 angle.gif

6x6x6 frontal.gif

data.py (10.6 KB)

dump.py (35.3 KB)

dump.xyz (259 KB)

pdb.py (9.18 KB)

silica.tabulated (121 KB)

sio2.data (72.2 KB)

sio2.in (539 Bytes)

sio2.py (2.13 KB)

sio2pore.py (69.9 KB)

10

I’m attaching some scripts for modeling the flow of water and ions thru a silica pore, but they are quite dated and come with no guarantees or support, so users please beware.

Paul

![1C3EJP8(OLS8%W88IIKGFX.png|646x141

11

I’m attaching some scripts for modeling the flow of water and ions thru a silica pore, but they are quite dated and come with no guarantees or support, so users please beware.

Paul

![1C3EJP8(OLS8%W88IIKGFX.png|646x141

12

I have some questions:
(1) Could you send me the script of the movie of the flow of water and
ions thru a silica pore ？I want to see details of the script.

​what kind of script are you talking about? paul just e-mailed you the
scripts and inputs he used.​ if you want to know how to visualize the
results from LAMMPS simulations, please see here:
http://lammps.sandia.gov/viz.html

(2) I see someone used compass force field and it's Epot potential
function in MS to calculate the interaction between silica with hydroxyl and
water molecules, is't right ? can I use them in lammps ?

​as was pointed out in the reply to that inquiry, yes.​ it is one option.

(3) What force field and potential function do you use ?
      Please give me some advice,thank you!

​the force field that paul used, is in his scripts. if you want find out
what is commonly used for these kinds of applications, your best chance is
to survey the published literature.​

​axel.​

![1C3EJP8(OLS8%W88IIKGFX.png|646x141

13

I have some questions:
(1) Could you send me the script of the movie of the flow of water and ions thru a silica pore ？I want to see details of the script.

If it helps, I have attached some instructions that explain how to
view a simulation trajectory using VMD+topotools
("README_visualize.txt"). Other options are listed at the link Axel
posted:
http://lammps.sandia.gov/viz.html

(2) I see someone used compass force field and it's Epot potential function in MS to calculate the interaction between silica with hydroxyl and water molecules, is't right ? can I use them in lammps ?

see below

(3) What force field and potential function do you use ?

Hopefully Paul provided a link to a paper where the force-field
parameters (and surface-charges) come from (for water interacting with
silica).

Otherwise, if there are no molecular-dynamics experts at your
university, then you will have to search for papers discussing
simulations of water+silica. (Try google.com, bing.com,
scholar.google.com, www.ncbi.nlm.nih.gov/pubmed,
www.stackexchange.com, webofknowledge.com.)
Not baidu.com)
   I personally don't see why it would be necessary to use the COMPASS
force-field for soil+water I am guessing that they used COMPASS
because it is probably one of the default force-fields available in
materials-studio. (But this is not my area of expertise.)

   It sounds like you have already received some good replies. You
will have to make this decision what force-field parameters and
charges to use.

Andrew

I don't know if it helps, but here is a list of tools people use to
build DATA files for LAMMPS simulations:
http://lammps.sandia.gov/prepost.html

README_visualize.txt (2.85 KB)

14

I don’t have further advice or scripts to offer you on this. Others on the list may have more to offer you, or you should work with your advisor for further advice.

Paul

![1C3EJP8(OLS8%W88IIKGFX.png|646x141

15

I don’t have further advice or scripts to offer you on this. Others on the list may have more to offer you, or you should work with your advisor for further advice.

Paul

![1C3EJP8(OLS8%W88IIKGFX.png|646x141

16

I don’t have further advice or scripts to offer you on this. Others on the list may have more to offer you, or you should work with your advisor for further advice.

Paul

![1C3EJP8(OLS8%W88IIKGFX.png|646x141

17

I want to konw which force field and potential function do you use ?

​paul already stated clearly that he doesn't want to give any further
advice or support for these inputs. if you cannot figure out what they are,
then you should not use them. in fact, then you probably need first some
more training.

if you *had* done your homework and done some research of the published
literature (and the LAMMPS mailing list archives), you should recognize BKS
as one of the possible parameterizations and also would have found that
paul has done a tabulation for it to deal with some quirks of the
analytical form.

if you open your eyes and read the input you'll see that this input
obviously uses a tabulated potential and the label BKS is a hint as big as
the mount everest which one this is. ​

I think the force field and potential function is the key to my
simulation. Please show me clearly, thank you very much

​actually, key to successful simulations is to know the basics well, and i
cannot help but think that that is your main issue here. if you would be
suitably knowledgeable, you would have been able to draw the same
conclusions that i just have laid out for you. now that you have as many
details as you should need, i suggest you hit the literature and dig up the
necessary publications (hint, hint: how about searching for papers
(co-)authored by paul or for BKS and sio2?)

if you still need enlightenment, then you should definitely have a chat
with your adviser and let your adviser be the source of your future wisdom.
that will save you and many others a lot of trouble.​

​axel.​

![1C3EJP8(OLS8%W88IIKGFX.png|646x141