On 10/30/13 1:46 PM, Guillaume Chevrot wrote:
Hi,
2013/10/30 Justin Lemkul
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
de
Hi,
2013/10/30 Justin Lemkul
>
>
> 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
> constrai
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, tha
: 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-
t to
~1e-6.
Should I send 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
>> >> S
> 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 mdru
rom: 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-u
> 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 iterati
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
>>
>> Al
...@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) tole
.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
&g
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 us
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 quest
> 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.
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 molec
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