[gmx-users] Polyethylene (PE) simulations in Gromacs - please!
Chansoo Kim
tree.csc at gmail.com
Tue Mar 3 15:42:20 CET 2009
Dear Justin and gmx-users:
Thank you for your answer, Justin.
Since I corrected error related to "blank" in the input files (pdb and
etc.), it has never given me "segmentation fault."
So... this problem is not related to this one anyway.
Now, I will try to correct others by following your suggestion.
After trying, I will contact you again... :)
Thank you again!!
Sincerely yours,
C Kim
On Tue, Mar 3, 2009 at 9:09 AM, Justin A. Lemkul <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>> 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
>
> ========================================
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
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