[gmx-users] Choosing water molecules and box type and dimensions

2016-04-29 Thread zeineb SI CHAIB
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

Re: [gmx-users] Choosing water molecules and box type and dimensions

2016-04-29 Thread abhijit Kayal
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

Re: [gmx-users] Choosing water molecules and box type and dimensions

2016-04-29 Thread Justin Lemkul
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

Re: [gmx-users] Choosing water molecules and box type and dimensions

2016-04-29 Thread zeineb SI CHAIB
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

Re: [gmx-users] Choosing water molecules and box type and dimensions

2016-04-29 Thread Justin Lemkul
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

Re: [gmx-users] Choosing water molecules and box type and dimensions

2016-04-29 Thread abhijit Kayal
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

Re: [gmx-users] Choosing water molecules and box type and dimensions

2016-04-29 Thread Smith, Micholas D.
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

Re: [gmx-users] Choosing water molecules and box type and dimensions

2016-04-29 Thread Justin Lemkul
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

Re: [gmx-users] Choosing water molecules and box type and dimensions

2016-04-29 Thread Smith, Micholas D.
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

Re: [gmx-users] Choosing water molecules and box type and dimensions

2016-05-02 Thread zeineb SI CHAIB
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.