Re: namd-l digest V1 #1282

From: Istvan Jonyer (istvan_at_rescale.com)
Date: Fri Jan 17 2014 - 14:04:39 CST

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On Thu, Jan 16, 2014 at 11:07 PM, namd-l digest <
owner-namd-l-digest_at_ks.uiuc.edu> wrote:

>
> namd-l digest Friday, January 17 2014 Volume 01 : Number 1282
>
>
>
> In this issue:
>
> namd-l: keeping Crystal angles constant
> AW: namd-l: keeping Crystal angles constant
> AW: namd-l: keeping Crystal angles constant
>
> ----------------------------------------------------------------------
>
> Date: Wed, 15 Jan 2014 23:33:58 +0530
> From: Mohan maruthi sena <maruthi.sena_at_gmail.com>
> Subject: namd-l: keeping Crystal angles constant
>
> Hi all,
> I want to simulate a crystal which has lengths a,b,c and angles
> alpha=90 deg, beta=97.4 deg and gamma=90 degrees. When I minimize the
> structure , i get a different structure whose alpha=90,beta =90 and
> gamma=90. My question is , How can i keep alpha,beta,gamma constant in my
> namd simulations. Do I have to mention any keyword in namd configurations
> file.
>
> Thanks for a reply in advance,
> Mohan
>
> ------------------------------
>
> Date: Thu, 16 Jan 2014 09:13:08 +0100
> From: "Norman Geist" <norman.geist_at_uni-greifswald.de>
> Subject: AW: namd-l: keeping Crystal angles constant
>
> You should mention what kind of crystal and what set of parameters you use.
> Do you have bond and angles defined or is it all nonbonded?
>
>
>
> Usually, if the crystal is periodic in all directions and the box size is
> correct, the angles shouldn't be able to deform. However, you might be
> interested in the extrabonds command in namd.
>
>
>
> Norman Geist.
>
>
>
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
> von Mohan maruthi sena
> Gesendet: Mittwoch, 15. Januar 2014 19:04
> An: namd-l_at_ks.uiuc.edu
> Betreff: namd-l: keeping Crystal angles constant
>
>
>
> Hi all,
>
> I want to simulate a crystal which has lengths a,b,c and angles
> alpha=90 deg, beta=97.4 deg and gamma=90 degrees. When I minimize the
> structure , i get a different structure whose alpha=90,beta =90 and
> gamma=90. My question is , How can i keep alpha,beta,gamma constant in my
> namd simulations. Do I have to mention any keyword in namd configurations
> file.
>
> Thanks for a reply in advance,
>
> Mohan
>
>
>
> - ---
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>
> ------------------------------
>
> Date: Thu, 16 Jan 2014 09:36:51 +0100
> From: "Norman Geist" <norman.geist_at_uni-greifswald.de>
> Subject: AW: namd-l: keeping Crystal angles constant
>
> If you want the crystal to periodic, the box size must fit with the crystal
> constants. Otherwise the crystal is squeezed or will probably expand what
> results in changed angles and average distances. Are there bonds and angle
> parameters for this crystal?
>
>
>
> Norman Geist.
>
>
>
> Von: Mohan maruthi sena [mailto:maruthi.sena_at_gmail.com]
> Gesendet: Donnerstag, 16. Januar 2014 09:34
> An: Norman Geist
> Betreff: Re: namd-l: keeping Crystal angles constant
>
>
>
> Hello Sir,
>
> Thanks for a reply, The crystal is monoclinic and I am using
> charmm parameters. The crystal is also periodic. I have given the correct
> box size. Can you just elaborate how to mention the box size for crystal.
>
> Thanks,
>
> Mohan
>
>
>
> On Thu, Jan 16, 2014 at 1:43 PM, Norman Geist
> <norman.geist_at_uni-greifswald.de> wrote:
>
> You should mention what kind of crystal and what set of parameters you use.
> Do you have bond and angles defined or is it all nonbonded?
>
>
>
> Usually, if the crystal is periodic in all directions and the box size is
> correct, the angles shouldn't be able to deform. However, you might be
> interested in the extrabonds command in namd.
>
>
>
> Norman Geist.
>
>
>
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
> von Mohan maruthi sena
> Gesendet: Mittwoch, 15. Januar 2014 19:04
> An: namd-l_at_ks.uiuc.edu
> Betreff: namd-l: keeping Crystal angles constant
>
>
>
> Hi all,
>
> I want to simulate a crystal which has lengths a,b,c and angles
> alpha=90 deg, beta=97.4 deg and gamma=90 degrees. When I minimize the
> structure , i get a different structure whose alpha=90,beta =90 and
> gamma=90. My question is , How can i keep alpha,beta,gamma constant in my
> namd simulations. Do I have to mention any keyword in namd configurations
> file.
>
> Thanks for a reply in advance,
>
> Mohan
>
>
>
>
>
> _____
>
>
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> ------------------------------
>
> End of namd-l digest V1 #1282
> *****************************
>
>

-- 
*Istvan Jonyer*
VP, Product Management
Rescale, Inc.
www.rescale.com
istvan_at_rescale.com
+1 (415) 816-7561
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