Re: [gmx-users] Build polymers with pdb2gmx

2020-01-27 Thread 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

--
==

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

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

==

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[gmx-users] Build polymers with pdb2gmx

2020-01-24 Thread Li, Shi 
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
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^^
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?

Thanks for your help and suggestions.

-- 

Shi Li

Research Assistant, Ph.D. Candidate
Department of Chemistry &
Center for Applied Energy Research (CAER)
University of Kentucky

Email: sli...@g.uky.edu
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