Saravanan= Hi

I think we are talking about two complete= ly different things here. If you want to construct a polymer crystal then t= he method offered by GaussView is perfectly fine. If you want to construct = an amorphous polymer (what you call 3D structure) then you cannot use Gauss= View as this will create only crystalline systems. In the latter case you n= eed to construct the polymer “by hand” or using alternative sof= tware.

Now regarding the problems you have wi= th the PBC tutorials I would recommend you don’t waste your time and = look for alternative software. VESTA is a good possibility http://jp-minerals.org/vesta/en/ and you c= an save the outputs as PDBs, but I am sure there are other packages (free o= r otherwise available).

I hope this helps

Thomas

<= p class=3DMsoNormal>

From: owner-chemistry+thomas.gkourmpis=3D= =3Dborealisgroup.com!^!ccl.net [mailto:owner-chemistry+thomas.gkourmpis=3D=3D= borealisgroup.com!^!ccl.net] On Behalf Of Sharan sara180681]-[gmail.co= m
Sent: Friday, October 05, 2012 7:50 PM
To: Gkourmpis,= Thomas
Subject: CCL:G: Polymer Construction

= Hi Gkourmpis Thomas

At first i would like to thank,= for you reply.

<= /o:p>

In Gauss View using Periodic Bound= ary Conditions (PBC) one can construct Polymer unit cell, after which super= cell is constructed. This resembles the whole polymer, is what my understa= nding. I don't think so the constrain of, number of repeating units comes i= nto picture.

But my problem is the steps given for building the unit cell= is not clear to me. There are 20 steps, using these steps i want to c= onstruct a polymer of my interest.

When you say &qu= ot;construct by hand are you referring to PBC or just regular 3D structure = of a monomer?

With regards

Saravanan

On Thu, Oct 4, 2012 at 4:02 PM, Gkourmpis= , Thomas Thomas.Gkourmpis##borealisgro= up.com <owner-chemistry=CCl.net> wrote:

Regarding = the polymer in Gaussian the question is how many repeating units you need. = If you need only a few units and each is small you can always construct it = by hand in GaussView. If on the other hand you want a “proper” = chain with many units then you’ll be better off if you use any of the= builders used in Molecular Dynamics packages and construct your system the= re. Then you can convert it to any file that Gaussian can read and use it a= s you see fit.

&nbs= p;

Have I answered yo= ur question or I misunderstood something?

= Thomas

From:= owner-chemistry+thomas.gkourmpis=3D=3Dborealisgroup.com-x-ccl.net [mailto:owner-chemistry+thomas.gkourmpis=3D=3Dborealisgroup.com-x-ccl.net] = On Behalf Of Sharan sara180681%%gmail.com
Sent: Thursday, October 04, 2012 10:59 AMTo: Gkourmpis, Thomas
Subject: CCL:G: Polymer Constructi= on

Can somebody help me in constructing Polymeric unit in Gaussian for op= timization. I am not clear on constructing the Translational vector for pol= ymeric unit. I went through the example given in Gaussian 03, I am not= clear on few fixed values supplied in the examples in constructing the pol= ymeric unit.

Some helping hand will be greateful.. thanks in advance.

With best re= gards

*************************************************
= Dr. I. SARAVANAN, M.Sc., M.Phil., PGDCA., PGDHRM., Ph.D.,<= br>Consultant,

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