Hi,
I was wondering if there is an option or a way to use the algorithm SHAKE
for the water molecules (instead of SETTLE).
Thanks!
Guillaume
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On 10/30/13 12:00 PM, Guillaume Chevrot wrote:
Hi,
I was wondering if there is an option or a way to use the algorithm SHAKE
for the water molecules (instead of SETTLE).
Never tried it, but I would assume
define = -DFLEXIBLE
constraint-algorithm = shake
would do the trick. Of course,
Hi,
2013/10/30 Justin Lemkul jalem...@vt.edu
On 10/30/13 12:00 PM, Guillaume Chevrot wrote:
Hi,
I was wondering if there is an option or a way to use the algorithm SHAKE
for the water molecules (instead of SETTLE).
Never tried it, but I would assume
define = -DFLEXIBLE
On 10/30/13 1:46 PM, Guillaume Chevrot wrote:
Hi,
2013/10/30 Justin Lemkul jalem...@vt.edu
On 10/30/13 12:00 PM, Guillaume Chevrot wrote:
Hi,
I was wondering if there is an option or a way to use the algorithm SHAKE
for the water molecules (instead of SETTLE).
Never tried it, but I
input files?
Thanks,
David
Berk
Berk
Date: Thu, 5 Feb 2009 22:41:47 +0100
From: sp...@xray.bmc.uu.se
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] shake for water
Berk Hess wrote:
Date: Thu, 5 Feb 2009 19:35:09 +0100
From: sp...@xray.bmc.uu.se
To: gmx
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] shake for water
Berk Hess wrote:
Date: Thu, 5 Feb 2009 19:35:09 +0100
From: sp...@xray.bmc.uu.se
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] shake for water
David Mobley wrote:
All,
A quick question on constraints... I'm using TIP4P-Ew
Berk,
Another question, just to be sure.
Have you actually checked that the other code really gets the distances
right up to 1e-12?
Yes.
Berk
Date: Thu, 5 Feb 2009 12:03:21 -0600
From: dmob...@gmail.com
To: gmx-users@gromacs.org
Subject: [gmx-users] shake for water
All,
A quick
No, it is not the square.
The code does a small 'a' approximation: (1+a)^2=1+2a+a^2 is approx 1+2a.
I have also tested/benchmark shake in gromacs for my first lincs paper
and the plincs paper and it always behaved the way I thought it would.
The problem is not that you need more iterations
-users] shake for water
Berk Hess wrote:
Date: Thu, 5 Feb 2009 19:35:09 +0100
From: sp...@xray.bmc.uu.se
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] shake for water
David Mobley wrote:
All,
A quick question on constraints... I'm using TIP4P-Ew in gromacs
Date: Mon, 9 Feb 2009 12:00:52 -0600
Subject: Re: [gmx-users] shake for water
From: dmob...@gmail.com
To: gmx-users@gromacs.org
Hi,
I don't agree.
It uses the small 1+a approximation for the square.
Also mdrun prints the rmsd determined with independent code,
which
All,
A quick question on constraints... I'm using TIP4P-Ew in gromacs 3.3.2
and am concerned with reproducing energies from another code very
precisely for several specific snapshots. I am doing a zero-step mdrun
of a setup with one small molecule and two tip4p-ew water molecules.
Anyway, I have
David Mobley wrote:
All,
A quick question on constraints... I'm using TIP4P-Ew in gromacs 3.3.2
and am concerned with reproducing energies from another code very
precisely for several specific snapshots. I am doing a zero-step mdrun
of a setup with one small molecule and two tip4p-ew water
Date: Thu, 5 Feb 2009 19:35:09 +0100
From: sp...@xray.bmc.uu.se
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] shake for water
David Mobley wrote:
All,
A quick question on constraints... I'm using TIP4P-Ew in gromacs 3.3.2
and am concerned with reproducing energies from
Hi,
Another question, just to be sure.
Have you actually checked that the other code really gets the distances
right up to 1e-12?
Berk
Date: Thu, 5 Feb 2009 12:03:21 -0600
From: dmob...@gmail.com
To: gmx-users@gromacs.org
Subject: [gmx-users] shake for water
All,
A quick question
Berk Hess wrote:
Date: Thu, 5 Feb 2009 19:35:09 +0100
From: sp...@xray.bmc.uu.se
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] shake for water
David Mobley wrote:
All,
A quick question on constraints... I'm using TIP4P-Ew in gromacs 3.3.2
and am concerned
: [gmx-users] shake for water
Berk Hess wrote:
Date: Thu, 5 Feb 2009 19:35:09 +0100
From: sp...@xray.bmc.uu.se
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] shake for water
David Mobley wrote:
All,
A quick question on constraints... I'm using TIP4P
...@hotmail.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] shake for water
Date: Thu, 5 Feb 2009 23:02:31 +0100
Hi,
I don't agree.
It uses the small 1+a approximation for the square.
Also mdrun prints the rmsd determined with independent code,
which is consistent with the (correct) tolerance
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