From: Raman Preet Singh (ramanpreetsingh_at_hotmail.com)
Date: Tue Aug 23 2022 - 07:03:28 CDT
Try CHARMM-GUI for polysaccharide structures including dextran. It generates CHARMM and AMBER FF files for NAMD and other MD programs.
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From: owner-namd-l-digest_at_ks.uiuc.edu <owner-namd-l-digest_at_ks.uiuc.edu> on behalf of namd-l digest <owner-namd-l-digest_at_ks.uiuc.edu>
Sent: Tuesday, August 23, 2022 3:35:56 PM
To: namd-l-digest_at_ks.uiuc.edu <namd-l-digest_at_ks.uiuc.edu>
Subject: namd-l digest V1 #3272
namd-l digest Tuesday, August 23 2022 Volume 01 : Number 3272
In this issue:
Re: namd-l: Simulating a system with an imaginary barrier
namd-l: Ficoll/Dextran CHARMM Force Field
Re: namd-l: Simulating a system with an imaginary barrier
----------------------------------------------------------------------
Date: Mon, 22 Aug 2022 11:35:03 +0200
From: Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
Subject: Re: namd-l: Simulating a system with an imaginary barrier
Hi Monika, please try the tclBC option.
Giacomo
On Thu, Aug 18, 2022 at 3:54 PM Monika Kumari <
Monika.Kumari_at_chemistry.iitd.ac.in> wrote:
> Dear all,
> I am trying to maintain an ion concentration gradient in a lipid
> membrane system. For this, I need to put an imaginary wall on one end of
> the box (restricting only the ions not water) so that the ions don't
> move to the other side via PBC. Also, the ions should move freely on one
> side of the membrane except for the restriction to cross the barrier.
> Can anyone suggest how to perform the simulation in NAMD?
> Thank you.
>
> Best regards,
> Monika
>
>
------------------------------
Date: Mon, 22 Aug 2022 19:14:27 +0000
From: Polly Ren <pollyren_at_uchicago.edu>
Subject: namd-l: Ficoll/Dextran CHARMM Force Field
Hello!
I was wondering whether anyone has the CHARMM force field for the Ficoll 70 or
Dextran 70 molecules? We are trying to perform a macromolecule crowding
simulation but we are unable to find the force field for either polymer. Any
guidance on where they could be found or how they can be constructed would be
greatly appreciated!
Thank you,
Polly Ren
------------------------------
Date: Tue, 23 Aug 2022 15:32:41 +0530
From: Monika Kumari <Monika.Kumari_at_chemistry.iitd.ac.in>
Subject: Re: namd-l: Simulating a system with an imaginary barrier
Thanks Dr. Giacomo, I'll try it.
On Mon, 22 Aug 2022 at 15:05, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:
> Hi Monika, please try the tclBC option.
>
> Giacomo
>
> On Thu, Aug 18, 2022 at 3:54 PM Monika Kumari <
> Monika.Kumari_at_chemistry.iitd.ac.in> wrote:
>
>> Dear all,
>> I am trying to maintain an ion concentration gradient in a lipid
>> membrane system. For this, I need to put an imaginary wall on one end of
>> the box (restricting only the ions not water) so that the ions don't
>> move to the other side via PBC. Also, the ions should move freely on one
>> side of the membrane except for the restriction to cross the barrier.
>> Can anyone suggest how to perform the simulation in NAMD?
>> Thank you.
>>
>> Best regards,
>> Monika
>>
>>
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>
> CAUTION: This email originated from outside of IIT Delhi. Do not click
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------------------------------
End of namd-l digest V1 #3272
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