ition of the harmonic
potential. Note that this is not used with constraints, only when you
have flexible models.
Gromacs uses degrees instead of radians in the user input.
Berk
Date: Tue, 14 Sep 2010 15:49:03 +0200
Subject: RE: [gmx-users] Regular vs. CHARMM TIP3P water model
rPres) and the density value extracted from the edr file by
>> g_energy. I obtain fairly similar results: 984.8 +/-4.5 for TIP3P and
>> 1015.0 +/- 3.6 for Charmm TIP3P.
>>
>> >
>> > I would expect that the difference with your number is mainly due to
>> the
airly similar results: 984.8 +/-4.5 for TIP3P and
> 1015.0 +/- 3.6 for Charmm TIP3P.
>
> >
> > I would expect that the difference with your number is mainly due to the
> > shorter LJ cut-off you are using.
> >
> > Berk
> >
> > From: g...@hotmail.com
you are using.
>
> Berk
>
> From: g...@hotmail.com
> To: gmx-users@gromacs.org
> Subject: RE: [gmx-users] Regular vs. CHARMM TIP3P water model
> Date: Tue, 14 Sep 2010 11:33:16 +0200
>
>
>
>
>
>
>
>
> Hi,
>
> I don't understand what exactly y
010 13:11:47 +0200
> Subject: RE: [gmx-users] Regular vs. CHARMM TIP3P water model
> From: nicolas.sa...@cermav.cnrs.fr
> To: gmx-users@gromacs.org
>
> >
> > Hi,
> >
> > I don't understand what exactly you want to reproduce.
> > Standard tip3p and Char
> Date: Tue, 14 Sep 2010 13:11:47 +0200
> Subject: RE: [gmx-users] Regular vs. CHARMM TIP3P water model
> From: nicolas.sa...@cermav.cnrs.fr
> To: gmx-users@gromacs.org
>
> >
> > Hi,
> >
> > I don't understand what exactly you want to reprod
act the density.
That's a good thing to know, I'll recalculate the density with g_energy.
>
> Berk
>
> From: g...@hotmail.com
> To: gmx-users@gromacs.org
> Subject: RE: [gmx-users] Regular vs. CHARMM TIP3P water model
> Date: Tue, 14 Sep 2010 11:58:31 +0200
>
>
sent in the GROMACS tips3p.itp file. So, a
better use of the CHARMM TIP3P model in GROMACS would be to add this
constraint in tips3p.itp and use Shake instead of Settle, isn't it?
>
>> Date: Tue, 14 Sep 2010 11:00:55 +0200
>> From: sp...@xray.bmc.uu.se
>> To: gmx-users@grom
@gromacs.org
Subject: RE: [gmx-users] Regular vs. CHARMM TIP3P water model
Date: Tue, 14 Sep 2010 11:58:31 +0200
Hi,
We did some checking.
The value of the density for tip3p reported in the Gromacs Charmm ff
implementation of 1001.7 is incorrect.
This should have been 985.7. The number of 1014.7
LJ cut-off you are using.
Berk
From: g...@hotmail.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] Regular vs. CHARMM TIP3P water model
Date: Tue, 14 Sep 2010 11:33:16 +0200
Hi,
I don't understand what exactly you want to reproduce.
Standard tip3p and Charmm tip3p are diff
x-users@gromacs.org
> Subject: Re: [gmx-users] Regular vs. CHARMM TIP3P water model
>
> On 2010-09-14 10.23, Nicolas SAPAY wrote:
> > Hello everybody,
> >
> > I have many difficulties to reproduce TIP3P simulation results with CHARMM
> > TIP3P. Regular TIP3P
On 2010-09-14 10.23, Nicolas SAPAY wrote:
Hello everybody,
I have many difficulties to reproduce TIP3P simulation results with CHARMM
TIP3P. Regular TIP3P gives systematically a lower density than its CHARMM
counterpart, independantly from the cutoff for non-bonded interactions,
the version of G
12 matches
Mail list logo
