From: Sindu (sindu_at_serc.res.in)
Date: Wed May 08 2013 - 03:46:35 CDT
Thank you for your advice sir. Now I will either put my time and effort to write a Tcl script or try to use MD codes where it has been implemented.
Regards,
B.S.Sindu
On 05/08/13 02:09 PM, Axel Kohlmeyer wrote:
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> On Wed, May 8, 2013 at 9:33 AM, Sindu <sindu_at_serc.res.in> wrote:
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> > 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.
> >
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> it can be done through the Tcl scripting features.
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> > 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.
> >
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> 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.
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> as the saying goes: there ain't no such thing as a free lunch.
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> axel.
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> >
> > Regards,
> > B.S.Sindu
> >
> > On 05/08/13 12:52 PM, Norman Geist wrote:
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> > > 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?
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> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>
> International Centre for Theoretical Physics, Trieste. Italy.
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