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

Chansoo Kim tree.csc at gmail.com
Tue Mar 3 14:49:53 CET 2009


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 fileEth     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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