[gmx-users] Polyethylene (PE) simulations in Gromacs - please!
Justin A. Lemkul
jalemkul at vt.edu
Tue Mar 3 16:13:43 CET 2009
Chansoo Kim wrote:
> Dear Justin:
>
>
> Please call me, 'chance'.
> I have been doing neutron scattering and MD on water.
> Thank you again for this conversation with you, Justin.
>
> Right now, I am trying to do polymer simulation to mimic an interaction
> with a plasma.
> To do so, I am targeting PE system.
>
> Related to the my question related to the [Error] and [Question #1],
>
> [Error]
> When I did run the pdb2gmx, I got the following error.
> "Atom -C2 not found in residue PEth1 while adding hydrogens"
>
You can't specify a previous residue (designated by -) from the first residue in
a chain. Hence why I suggested what I did before about special terminal
residues. See the post I just sent about functioning .rtp and .hdb entries,
they worked for me.
-Justin
> [Question #1]
> Therefore, what I should define more...?
>
> I cannot avoid to ask you this question again!
>
> As I emailed you, since I corrected error related to "blank" in the
> input files (pdb and etc.), it has never given me "segmentation fault."
> The only error that the gromacs gives me is the above one.
>
> Even though I am following your suggestion in the previous email, I want
> to clarify the above problem.
>
> Do you have any idea on this...?
>
> Thank you again!!
>
>
> Sincerely yours,
>
> Chance
>
>
> (PS) The "chemical reaction", which I wrote in the second email, is my
> mistake. I did not mean "chemical reaction"... And I appreciate that you
> pointed it out.
>
>
>
> On Tue, Mar 3, 2009 at 9:09 AM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> 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>
> <mailto: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> <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 <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
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