Hi,
I'm working on a protein and two cofactors and one substrate, I have too
simulate all this system on GROMACS. I'm in the first stage: choosing a force
field, box type and dimensions, water molecules...etc.
I would like to know more about the water molecule types (I looked on the
internet
you can look the following paper for the properties of different water
models.
Simulating water with rigid non-polarizable models: a general perspective
Phys. Chem. Chem. Phys., 2011, 13, 19663–19688.
In this paper they compare all the water models based on their different
thermodynamics and
dyna
On 4/29/16 9:17 AM, abhijit Kayal wrote:
you can look the following paper for the properties of different water
models.
Simulating water with rigid non-polarizable models: a general perspective
Phys. Chem. Chem. Phys., 2011, 13, 19663–19688.
In this paper they compare all the water models bas
Dear all,
Thank your for your answers.
@ Justin,
Where can I found informations related to the compatibility of one water type
with the force field that I choose for my protein? in other words "where can I
found information about the water type that had been used for the
parametrisation of
On 4/29/16 9:51 AM, zeineb SI CHAIB wrote:
Dear all,
Thank your for your answers.
@ Justin,
Where can I found informations related to the compatibility of one water type with the
force field that I choose for my protein? in other words "where can I found
information about the water type th
Justin, as always is absolutely right. The paper that I have suggested is
just compare the different water models with the bulk properties. And the
bio molecular forcefields are compatible with particular type water
model. Like charmm force field is compatible with TIP3P water.
On Fri, Apr 29, 2
Kayal
Sent: Friday, April 29, 2016 10:07 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Choosing water molecules and box type and dimensions
Justin, as always is absolutely right. The paper that I have suggested is
just compare the different water models with the bulk properties. And the
on behalf of abhijit Kayal
Sent: Friday, April 29, 2016 10:07 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Choosing water molecules and box type and dimensions
Justin, as always is absolutely right. The paper that I have suggested is
just compare the different water models with the
red.
-Justin
> -Micholas
>
>
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> on behalf of abhijit
> Kayal
> Sent: Friday, April 29, 2016 10:07 AM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Choosing water molecules and box type and dimen
Dear all,
Thank your for your answers.
@ Justin,
Actually I was hesitating between CHARMM and Amber force fields, I hadn't
enough informations from my tutors. Finally I'm going with CHARMM 27, it is the
most convenient in my case.
Thank you again for your orientation.
Zeineb.
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