rigid model.
Mark
Sanku
*From:* David van der Spoel
*To:* Discussion list for GROMACS users
*Sent:* Fri, April 29, 2011 11:46:01 AM
*Subject:* Re: [gmx-users] rigid tetrahedral molecule
On 2011-04-29 17.55, gyorgy.han...@fc.up.pt
<mailto:gyorgy.han...@fc.up.pt> wrote:
&g
r can be implemented, however.
Mark
Sanku
*From:* David van der Spoel
*To:* Discussion list for GROMACS users
*Sent:* Fri, April 29, 2011 11:46:01 AM
*Subject:* Re: [gmx-users] rigid tetrahedral molecule
On 2011-04-29 17.55, gy
r can be implemented, however.
Mark
Sanku
*From:* David van der Spoel
*To:* Discussion list for GROMACS users
*Sent:* Fri, April 29, 2011 11:46:01 AM
*Subject:* Re: [gmx-users] rigid tetrahedral molecule
On 2011-04-29 17.55, gy
ule 'rigid' might be good enough.
But, gromacs does not explicitly do rigid body MD. That's why I was
looking for
a trick .
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Sent: Wed, April 27, 2011 8:25:05 PM
Subject: Re: [gmx-users
details of how to use
virtual sites for a tetrahedral molecule. It would have been helpful.
Sanku
From: David van der Spoel
To: Discussion list for GROMACS users
Sent: Fri, April 29, 2011 11:46:01 AM
Subject: Re: [gmx-users] rigid tetrahedral molecule
On
__
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Sent: Wed, April 27, 2011 8:25:05 PM
Subject: Re: [gmx-users] rigid tetrahedral molecule
Sanku M wrote:
Hi,
I am interested in simulating a anionic molecule BF4(-) ( Boron
tetrafluoride). In the paper whi
___
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Sent: Wed, April 27, 2011 8:25:05 PM
Subject: Re: [gmx-users] rigid tetrahedral molecule
Sanku M wrote:
Hi,
I am interested in simulating a anionic molecule BF4(-) ( Boron
tetrafluoride). In the paper which developed the param
.
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Sent: Wed, April 27, 2011 8:25:05 PM
Subject: Re: [gmx-users] rigid tetrahedral molecule
Sanku M wrote:
Hi,
I am interested in simulating a anionic molecule BF4(-) ( Boron
tetrafluoride). In the
BF4F4 1 -0.4569
*From:* Mark Abraham
*To:* Discussion list for GROMACS users
*Sent:* Thu, April 28, 2011 1:00:42 AM
*Subject:* Re: [gmx-users] rigid tetrahedral molecule
On 4/28/2011 3:49 PM, Sanku M
pled bond constraints) because it is fiddly to
get such things right (and fast).
Mark
*From:* Mark Abraham
*To:* Discussion list for GROMACS users
*Sent:* Wed, April 27, 2011 11:14:34 PM
*Subject:* Re: [gmx-users] rigid
: Mark Abraham
To: Discussion list for GROMACS users
Sent: Thu, April 28, 2011 1:00:42 AM
Subject: Re: [gmx-users] rigid tetrahedral molecule
On 4/28/2011 3:49 PM, Sanku M wrote:
I went through the LINCS manual . But, I am still struggling with
coming up with the idea of putting correct
to get such
things right (and fast).
Mark
*From:* Mark Abraham
*To:* Discussion list for GROMACS users
*Sent:* Wed, April 27, 2011 11:14:34 PM
*Subject:* Re: [gmx-users] rigid tetrahedral molecule
On 4/28/2011 1:54 PM
GROMACS users
Sent: Wed, April 27, 2011 11:14:34 PM
Subject: Re: [gmx-users] rigid tetrahedral molecule
On 4/28/2011 1:54 PM, Sanku M wrote:
Hi,
> I tried to keep the geometry of the BF4 fixed by using constraints
>using lincs. But , unfortunately, my simulation is cr
1 34 5
3 1 24 5
4 1 23 5
5 1 23 4
*From:* Mark Abraham
*To:* Discussion list for GROMACS users
*Sent:* Wed, April 27, 2011 8:39:23 PM
*Subject:* Re: [
23 5
5 1 23 4
From: Mark Abraham
To: Discussion list for GROMACS users
Sent: Wed, April 27, 2011 8:39:23 PM
Subject: Re: [gmx-users] rigid tetrahedral molecule
On 4/28/2011 11:25 AM, Justin A. Lemkul wrote:
>
>
> Sanku M wro
25:05 PM
Subject: Re: [gmx-users] rigid tetrahedral molecule
Sanku M wrote:
> Hi,
> I am interested in simulating a anionic molecule BF4(-) ( Boron
>tetrafluoride). In the paper which developed the parameters for this
>molecule,
>it is mentioned that it has been used as '
On 4/28/2011 11:25 AM, Justin A. Lemkul wrote:
Sanku M wrote:
Hi,
I am interested in simulating a anionic molecule BF4(-) ( Boron
tetrafluoride). In the paper which developed the parameters for this
molecule, it is mentioned that it has been used as 'rigid' molecule
i.e the molecule only
Sanku M wrote:
Hi,
I am interested in simulating a anionic molecule BF4(-) ( Boron
tetrafluoride). In the paper which developed the parameters for this
molecule, it is mentioned that it has been used as 'rigid' molecule i.e
the molecule only has non-bonding interaction but there was no
i
Hi,
I am interested in simulating a anionic molecule BF4(-) ( Boron
tetrafluoride). In the paper which developed the parameters for this molecule,
it is mentioned that it has been used as 'rigid' molecule i.e the molecule only
has non-bonding interaction but there was no intramolecular motion
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