Re: AW: Bulk properties of polymers

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed May 08 2013 - 03:39:25 CDT

On Wed, May 8, 2013 at 9:33 AM, Sindu <sindu_at_serc.res.in> wrote:

> Dear Norman Geist,
> I want to simulate a box of specific volume containing monomers which are
> randomly distributed. Then I have to pull or push the box with a certain
> force in a particular direction.
> I have seen this kind of simulations being performed using other MD
> packages. But in NAMD I have not seen such simulations being done by
> anyone.
> So, I am not sure if it can be done.
>

it can be done through the Tcl scripting features.

> Also not getting a clue how to do it. If you give me some guidelines on
> how to do it, it will be extremely useful.
>

well, since nothing prefabricated exists, you'll either have to "clue
yourself in" by spending some time reading the docs and figuring out how to
do what you want to do with the features available. NAMD wasn't implemented
with these kind of applications in mind, so it will take some effort on
your site. also, if you want to do something that is not commonly done, it
is just natural that you cannot expect much specific help. so if you *do*
want to use NAMD, you *do* have to invest the time and effort to implement
the tools you need.

as the saying goes: there ain't no such thing as a free lunch.

axel.

> Regards,
> B.S.Sindu
>
>
> On 05/08/13 12:52 PM, *Norman Geist * ** wrote:**
>
> Hi Sindu,****
>
> ** **
>
> I don’t see a reason why you wouldn’t be able get the required data out of
> NAMD simulations of your polymers. If you have doubts, please explain more.
> ****
>
> ** **
>
> Regards****
>
> ** **
>
> Norman Geist.****
>
> ** **
>
> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Sindu
> *Gesendet:* Mittwoch, 8. Mai 2013 06:34
> *An:* namd-l_at_ks.uiuc.edu
> *Betreff:* namd-l: Bulk properties of polymers****
>
> ** **
> Hi all,****
> Can we determine the bulk properties (like Young's modulus, shear modulus)
> of polymers using NAMD?****
>
>

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.

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