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

[Justin A. Lemkul]

Chansoo Kim wrote:
> 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...
> 

No chemical reactions occur :)  See comments embedded below

> 
> [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
> 

Note that the message you referenced in your first post (which provided you with 
this .rtp entry) resulted in a segmentation fault, therefore indicating that it 
probably won't work.

> 
>    (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?

+ means next residue, - means previous.

> 
> 
> [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).
> 

Right, because H positioning in a polymer chain may depend on previous (-) or 
subsequent (+) residues, so the code doesn't know where to put them.

> 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...?
> 

Knowing that many people have tried to define PE with .tdb entries (and I think 
success is limited), I would suggest the following.  Define distinct .rtp 
entries for the caps of your chain.  Don't bother with -n.tdb and -c.tdb; I 
don't know how well the Gromacs code handles non-protein termini (maybe it 
works, but it seems to give fits for polymers).  The .rtp entry for PE you've 
shown above seems reasonable enough for a PE monomer within the chain, but may 
require some tweaking (since I've never tried, I don't know).

-Justin

> 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 
> <mailto: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 <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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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

========================================