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
>
>
>
> - ---
> Diese E-Mail ist frei von Viren und Malware, denn der avast! Antivirus
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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 ================================================== This email is confidential and may be privileged. If you have received it in error, please notify us immediately and then delete it. Please do not copy it, disclose its contents or use it for any purpose. ==================================================
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