[gmx-users] Polyethylene (PE) simulations in Gromacs - please!

Zuzana Benkova upolzben at savba.sk
Tue Mar 3 15:12:40 CET 2009


Dear Chansoo Kim,

It has passed relatively long time since I attempted to use pdb2gmx to build
my topology for polyethylene. I prepared the relevant files according to
those used for amino acids. I used + and - sign to discern the direction of
connectivity. I have encountered dome problems mentioned in the mail but
they have not been answered satisfactorily. Later on I wanted to run just
united atom simulations and I had next problem with pdb2gmx that always
include hydrogen atoms to my topology though I used option which should have
disabled this. I decided to build my topology file without pdb2gmx and I
applied force field that is not present in GMX directories. 

 

  _____  

From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Chansoo Kim
Sent: Tuesday, March 03, 2009 2:50 PM
To: jalemkul at vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] Polyethylene (PE) simulations in Gromacs - please!

 

Dear Justin:

 

 

Thank you for your reply.

I was too urgent, so I did not clarify my questions.

Sorry about that.

 

I totally understand how topology files (tdb, hdb, and etc..) work, but I do
not clearly understand chemical reaction, which I have to define in those
files...

 

 

[Situation]

I want to do simulate polyethylene (PE) using Gromacs and OPLS-AA force
field...

 

[Topology files and etc]

  (1) rtp file

[ Eth ]
 [ atoms ]
   C1    opls_136    -0.120    1
   H11   opls_140     0.060    1
   H12   opls_140     0.060    1
   C2    opls_136    -0.120    2
   H21   opls_140     0.060    2
   H22   opls_140     0.060    2
 [ bonds ]
   C1    H11
   C1    H12
   C1    C2
   C2    H21
   C2    H22
   C2    +C1
 
  (2) hdb file
Eth     2
2       6       H1       C1      C2     +C1
2       6       H2       C2      C1     -C2

 

 
  (3) -c.tdb file
 
[ Eth ]
[ replace ]
C1      opls_135        12.011  -0.18
[ add ]
3        4      H1      C1      C2
         opls_140       1.008   0.06
[ delete ]
H21
H22

 

 
  (4) -n.tdb file
 
[ Eth ]
[ replace ]
C2      opls_135        12.011   -0.18
[ add ]
3        4      H2      C2      C1
         opls_140       1.008   0.06
[ delete ]
H21
H22

 

   (5) input pdb file

 

ATOM      1  C1  Eth     1       1.000   1.540   0.000

ATOM      2  C2  Eth     1       2.456   2.041   0.000
ATOM      3  C1  Eth     2       2.456   3.581   0.000
ATOM      4  C2  Eth     2       3.912   4.083   0.000
ATOM      5  C1  Eth     3       3.912   5.623   0.000
ATOM      6  C2  Eth     3       5.368   6.124   0.000
END

 

[Error]

When I did run the pdb2gmx, I got the following error.

"Atom -C not found in residue PEth1 while adding hydrogens"

 

[Question #1 and #2]

Therefore, what I should define more...?

What does the "+" and "-" mean here?

 

 

[If...]

If I change the hdb file as follows,

 

 
Eth     2
2       6       H1       C1      C2     C1
2       6       H2       C2      C1     C2

 

After doing pdb2gmx, I got only 12 H-atoms (which means my terminal did NOT
work...).

And those positions are all (0, 0, 0).

 

Following is the results,

 

LE     Giving Russians Opium May Alter Current Situation

MODEL        1

ATOM      1  C1  PEt     1       1.000   0.000   0.000  1.00  0.00

ATOM      2  H11 PEt     1       0.000   0.000   0.000  1.00  0.00

ATOM      3  H12 PEt     1       0.000   0.000   0.000  1.00  0.00

ATOM      4  C2  PEt     1       2.450   6.000   1.000  1.00  0.00

ATOM      5  H21 PEt     1       0.000   0.000   0.000  1.00  0.00

ATOM      6  H22 PEt     1       0.000   0.000   0.000  1.00  0.00

ATOM      7  C1  PEt     2       2.450   6.000   1.000  1.00  0.00

ATOM      8  H11 PEt     2       0.000   0.000   0.000  1.00  0.00

ATOM      9  H12 PEt     2       0.000   0.000   0.000  1.00  0.00

ATOM     10  C2  PEt     2       3.910   2.000   3.000  1.00  0.00

ATOM     11  H21 PEt     2       0.000   0.000   0.000  1.00  0.00

ATOM     12  H22 PEt     2       0.000   0.000   0.000  1.00  0.00

ATOM     13  C1  PEt     3       3.910   2.000   3.000  1.00  0.00

ATOM     14  H11 PEt     3       0.000   0.000   0.000  1.00  0.00

ATOM     15  H12 PEt     3       0.000   0.000   0.000  1.00  0.00

ATOM     16  C2  PEt     3       5.360   8.000   4.000  1.00  0.00

ATOM     17  H21 PEt     3       0.000   0.000   0.000  1.00  0.00

ATOM     18  H22 PEt     3       0.000   0.000   0.000  1.00  0.00

TER

ENDMDL

 

[Question #3 from If... section ]

I guess that I have to change hdb and tdb files.

Would you please give some guide on that...?

 

Thank you for your care!

 

 

Sincerely yours,

 

C Kim

 

On Tue, Mar 3, 2009 at 8:35 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:



Chansoo Kim wrote:

Dear Dr. Benkova and others:


I am C. Kim and trying to simulation polymer system.

Since I guessed that polyethylene (PE) is a simple system, it could be not
that hard to simulate it in Gromacs.
Trying to do, I have read Dr. Benkova's articles in gmx-users mailing list
to tackle my problems.
Sorry to say, I could not solve problems, so I am asking your help!

Actually I have used your files written in followings,

http://www.mail-archive.com/gmx-users@gromacs.org/msg12204.html

[Q1]
After getting the result from the pdb2gmx, I could not see any H-atoms in my
system.
All the H-atoms have 0, 0, 0 positions!
Therefore, my question is
  how I should define hdb?

 

The .hdb file format is explained in the manual.

 


[Q2]
When I use -C2, and +C1 in hdb file, I always meet error.

 

What is the error?

-Justin

Is there any other things to add to the ffopls*.* files...?

Thank you for your care!


Sincerely 
C. Kim



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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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