[gmx-users] Build polymers with pdb2gmx

[Justin Lemkul]

On 1/24/20 3:20 PM, Li, Shi wrote:
> Dear GMX users,
>
> I am new to polymer simulation and want to build a polymer system for
> Gromacs. I have followed Justin's instruction to make polyethylene by
> editing the rtp and hdb file. But I have a couple of questions regarding a
> larger polymer configuration:
>
> 1. The example system (polyethylene) only has one repeat unit, is there a
> way to define the number of repeat unit and then generate the PDB file? I

GROMACS has no ability to build molecules.

> am also wondering if there is a way to make the configuration with random
> torsion? I currently use Gaussview to copy and paste, and the initial PDB
> is just a linear chain. Like this...^^O^^O^^O^^

Make the linear chain and run a Langevin simulation in the gas phase.

> 2. Since the PDB file is straightly from Gaussview, the atom names in the
> file are all in basic form (C, H, O...), in order for the pdb2gmx to work,
> I have to manually match and replace them according to the .rtp file. For
> larger repeat unit, is there a better way to do this?

Unfortunately, no. Software that outputs repetitive atom names makes 
your life a nightmare when actually trying to do a simulation.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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