Re: [gmx-users] Re: Carbon Nanotube Simulation Issues

Yang Ye Fri, 27 Jul 2007 01:46:34 -0700

On 7/27/2007 4:53 AM, Christopher Stiles wrote:

Ok here is the update:
I have made the following changes:
I almost doubled my box size and limited the saturation to 256 water
molecules.
I removed the include from my *.mdp file
Changed the includes in my topology file to:
#include "ffgmx.itp"
#include "spc.itp"
And added the following line of code to the [ bondtype ] section of the
ffgmxbon.itp file:
C    C    1   0.14210     478900.


I use the files in this zip file to run grompp:

http://cs86.com/CNSE/SWNT.zip

running grompp I use the following command:
grompp -f mdout_test.mdp -c SWNT_6_6_144_b4em.gro -p SWNT_6_6_144.top
-maxwarn 10000 -pp

What's the warnings?

It works but there is 1176 warnings, which I am assuming this is a problem?
Then I run mdrun using the following command:
Mdrun -s topol.tpr
It works just fine
Then I can view it with ngmx using the following command:
ngmx -f traj.xtc -s topol.tpr.
This works just fine as well.

My question is are the warnings ok/normal or is there some fix that needs to
be made?

Thank you again Yang, Bob, and every one else you have all been a great
help!

~Christopher Stiles
College of Nanoscale Science and Engineering (CNSE)
State University of New York, Albany, New York 12203, USA

________________________________________________

You shall include ffgmx.itp only and make change to ffgmxbon.itp.

On 7/27/2007 12:18 AM, Christopher Stiles wrote:

Yang & Bob,

When I change the include to be ffgmxbon.itp instead of ffgmx.itp I get

the

following error:
****************************
Fatal error:
Invalid order for directive bondtypes, file ""ffgmxbon.itp"", line 1
****************************
I believe it is because when just including ffgmxbon.itp it never calls

up

ffgmxnb.itp so there for atomtypes are not defined first ect...
Although my understanding of this whole process is very limited...

Thank you all very much for your patience and guidance helping me along!

~Christopher Stiles
College of Nanoscale Science and Engineering (CNSE)
State University of New York, Albany, New York 12203, USA

________________________________________________

-----Original Message-----
From: [EMAIL PROTECTED] [mailto:gmx-users-

[EMAIL PROTECTED]

On Behalf Of Yang Ye
Sent: Thursday, July 26, 2007 11:34 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Re: Carbon Nanotube Simulation Issues

Hi,

It's my typo again. Sorry. It shall be ffgmxbon.itp.

On 7/26/2007 10:57 PM, Christopher Stiles wrote:

Yang,
        Thank you again for being so detailed. I do have 2 questions though,
when you say:

So you shall change ffG43b1.itp to ffgmx.itp. And add the line
C    C    1   0.14210     478900.

To the end of section [ bondtypes ], not the end of the whole file.

You mean in the topology file I assume for the changing from

ffG43b1.itp

to

ffgmx.itp. But the adding of the line is what I am having trouble with,
should it go in the topology file or ffgmx.itp? because neither have a
[ bondtypes ] section and when I add one it just gives me errors. From

what

I understand from the manual it is only the *.itp files that can have

those

sections, so I think maybe it should go in the ffgmx.itp file I am just

not

making the addition to the file properly.
Also here is a copy of the ffgmx.itp file:
########################
#define _FF_GROMACS
#define _FF_GROMACS1

[ defaults ]
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
  1             1               no              1.0     1.0

#include "ffgmxnb.itp"
#include "ffgmxbon.itp"
########################
And here is a copy of my ffG43b1.itp file:
########################
#define _FF_GROMOS96
#define _FF_GROMOS43B1

[ defaults ]
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
  1             1               no              1.0     1.0

#include "ffG43b1nb.itp"
#include "ffG43b1bon.itp"
########################

Last of all this question is to any one, how do I reply to a specific
thread? I have searched around and I have had no luck.

Thank you so much for all of your help!

~Christopher Stiles
College of Nanoscale Science and Engineering (CNSE)
State University of New York, Albany, New York 12203, USA

_______________________________________________________

Hi,

I missed one dash in the front. So it should be

include = -IffG43b1.n2t

The problem you had was because of improper usage of include, for every

item

to be put in include=, you shall prefix -I in the front. Since you have

not

put it, cpp couldn't finish parsing the topology file, so your topology
contains nothing.

ffG43b1.n2t is not necessary for grompp.

You shall include spc.itp in your topology file to include the topology

for

water. So your file header shall be like

#include "ffG43b1.itp"
#include "spc.itp"

Last and most important, the line you added to ffgmxbon.itp is useless
because you are using GROMOS96 force field.

So you shall change ffG43b1.itp to ffgmx.itp. And add the line
C    C    1   0.14210     478900.

To the end of section [ bondtypes ], not the end of the whole file.

So the command line without -maxwarn can work properly. Note that you

shall

not use -maxwarn in most cases.
grompp -f mdout_test.mdp -c SWNT_6_6_144_b4em.gro -p
SWNT_6_6_144_post_genbox.top -pp

The suffix _s is just what I have specified for my build. You don't

need

the

same setting.

Regards,
Yang Ye


On 7/25/2007 10:29 PM, Christopher Stiles wrote:

Yang,
Thank you very much for you help. I am sorry I did not think to

package

my

files and commands up I will do so by the end of the day. As to the
ffG43b1.n2t it was to get x2top to work, it defines single and double

bonded

carbon so that I do not have to cap my tube with hydrogen. Although I

am

not

sure how you got the include to work with:
include = IffG43b1.n2t
Do you have a file named IffG43b1.n2t in your lib or your working dir?
The file comes from the ffgmx.n2t file in the Gromacs lib but the name

is

changes to ffG43b1.n2t and the following 2 lines are added:
C       C       1       C                         ; CNT Carbon with

one

bond

C       C       2       C       C                ; CNT double bonded

Carbon

Next must I use grompp_s? (I believe this is grompp with single

accuracy,

correct?) Because if so I will have to compile it.
Last question, by it gives a pass do you mean you get a little over

warnings and then get the following:
Fatal error:
No such moleculetype SOL

Thank you so much for your help I really appreciate it,

~Christopher Stiles
College of Nanoscale Science and Engineering (CNSE)
State University of New York, Albany, New York 12203, USA

Hi,

Sorry that most of us on the list were too busy to read one full page

of

details and download individual files. We might just prefer to

download

one package, and run a script file for us quickly dive into the

problem.

Is include in mdout_test.mdp a standard option? Where did you get it?

changed it to

include = IffG43b1.n2t

It works. Otherwise, cpp terminates before it generates a full top.
grompp -pp is always a good friend for grompp error (and thorough
reading of chapter 5 of manual).

Next issue comes the format of ffG43b1.n2t. I don't think it conforms

to

any GROMACS topology format. Again where does it comes from?

My grompp command line:
grompp_s -f mdout_test.mdp -c SWNT_6_6_144_b4em.gro -p
SWNT_6_6_144_post_genbox.top -maxwarn 10000000 -pp

It gives a pass, at least.

Hope you can work further on.

Regards,
Yang Ye

On 7/25/2007 2:41 AM, Christopher Stiles wrote:

I am trying to simulate a single wall carbon nanotube in a box
solvated in water, at 300k for about 200ps. Also once I accomplish
this I wish to fix either one end of the tube or fix the center of
mass position, although this part is unimportant if I can not get

the

thing to run at all yet.

I have created a page with a full detailed account of what I have

done

and tried so far. http://cs86.com/CNSE/SWNT.htm

Please note all files where created with Vim in the unix environment
so I think I have eliminated the formatting issues.

Also that I have tried the simulation with many different sized

tubes

from TubeGen (http://turin.nss.udel.edu/research/tubegenonline.html

),

both with and without hydrogen capped ends (this is something I have
read in the archives as a possible solution, it makes no difference

in

the end).

I have come to the conclusion through the help of many of you that

the

*.pdb file from TubeGen and mainly the residue UNK among other
things. If any one has had luck with using a TubeGen file to create

simulation please let me know as to how. Other wise I am looking at

few new options basically all of them involve writing my own files.

I guess I am looking for advice where to go from here.

~Christopher Stiles
College of Nanoscale Science and Engineering (CNSE)
State University of New York, Albany, New York 12203, USA

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Re: [gmx-users] Re: Carbon Nanotube Simulation Issues

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