[gmx-users] building up a long polymer chain

Justin A. Lemkul jalemkul at vt.edu
Fri Jun 18 21:44:28 CEST 2010

Moeed wrote:


> for PE. or maybe this dies not affect the results since charges and mass 
> are the same..?!

You can set the charges to whatever you want them to be, so this is no issue at all.

> Also: can opls_157 be used for both CH3 & CH2,on PE chain? what is the 
> suitable atom type for carbon atoms on PE chain?

The nonbonded parameters (sigma and epsilon) for opls_135 and opls_157 are 
identical.  I don't know why there are different types, but they are the same. 
Check ffoplsaanb.itp and you will see.


> The top file I got has contains exactly the same listing of [bonds] 
> [pairs] [angles] [dihedrals] as the one I got from the structure file 
> for which I did the numbering by hand. But I am unsure of the forcefield 
> parameters if they are extracted from itp file properly because after 
> doing energy minimization step I get LINCS error.

I don't fully understand what you did or what you think is wrong, but I do 
recall giving you some very thorough procedures to go through to diagnose a 
crashing system.  I even updated the wiki to keep track of all the tips I gave you.


> Q 2-1 Please kindly furnish me with your comments on this issue. *I need 
> a residue for internal ethylene monomer in rtp file which depends as 
> less as possible on atoms numbering (H11,...). *I think the solution 
> will help many gmx users dealing with polymers. what would be the best 
> approach?

To build a long polymer chain, it should be possible by generating a coordinate 
file of one monomer that is aligned with one of the principal axes and 
positioned such that its atoms are half a bond length from the edges of the box. 
  Then use genconf -nbox to replicate this system in one direction and you'll 
have as long a chain as you want, correctly numbered and named, and if you've 
done your geometry right, the structure will even be in a reasonable configuration.

If you want to use .rtp files to create a topology, atom naming is required to 
be consistent with the structure file.  There is no way around this.  The 
hydrogen atoms are actually very easy to deal with if you have an appropriate 
.hdb file, which is provided in the example you've been using for several weeks 
now.  So you really don't even need H atoms in your input file, just 
appropriately-named carbons.

> my current internal repeating unit has numbering of atoms:
> [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    -C2
>    C1    H11
>    C1    H12
>    C1    C2
>    C2    H21
>    C2    H22
>    C2    +C1
> Q 2-2. Does x2top command have advantage over pdb2gmx command with 
> regards to atom numbering?

It seems like your first real problem is creating a properly-formatted 
coordinate file.  If you have to add in residue names yourself and rename all of 
the atoms yourself, then that's more trouble than its worth.  See the above 
comment about genconf.


> Many many thanks,
> Best,
> Moeed


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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