Dear Gromacs Users
I would like to suggest a project in free energy calculations which can be in
cooperation.
The project is to demonstrate a novel and interesting method to calculate free
energy differences between two solvation/binding processes.
The first simulations are rather simple (solvat
-boun...@gromacs.org] on behalf
of Justin Lemkul [jalem...@vt.edu]
Sent: Saturday, September 22, 2012 10:35 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] force field parameters
On 9/22/12 2:13 PM, Asaf Farhi wrote:
> Dear Justin
>
> Thank you very much for the reply.
>
, September 22, 2012 3:53 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] force field parameters
On 9/22/12 8:48 AM, Asaf Farhi wrote:
> Dear Users
>
> Hi. I'm looking for a a list of bond stretching parameters for the potential
> 0.5k(r-r_eq)^2 that has units (k
Dear Users
Hi. I'm looking for a a list of bond stretching parameters for the potential
0.5k(r-r_eq)^2 that has units (k and r_eq).
Can anyone help me with that (article will be good)?
Thanks in advance,
Best regards,
Asaf
p.s it can be of any force field as long as there's list.
--
gmx-users m
GROMACS users
Subject: Re: [gmx-users] Question about Thermodynamic Integration
On 8/8/12 11:25 AM, Asaf Farhi wrote:
> Dear Justin
>
> Thank you very much for the reply.
> I want to understand how to calculate binding free energy difference of both
> molecules to another molecule.
rmodynamic Integration
On 8/8/12 6:35 AM, Asaf Farhi wrote:
> Dear Justin
>
> Thank you very much for the reply.
> It's written in the manual:
>
> 5.7.4 Topologies for free energy calculations
> Free energy differences between two systems, A and B, can be calculated as
&
This is why I still don't understand.
Best regards,
Asaf
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Asaf Farhi [asaf.fa...@weizmann.ac.il]
Sent: Wednesday, August 08, 2012 1:35 PM
To: Discussion list for GROMACS
users
Subject: Re: [gmx-users] Question about Thermodynamic Integration
On 8/8/12 3:11 AM, Asaf Farhi wrote:
> Dear Gromacs users
>
> Hi. I wanted to ask about the use of Thermodynamic Integration.
> If the two compared molecules have a different number of atoms (e.g
> Theophylli
Dear Gromacs users
Hi. I wanted to ask about the use of Thermodynamic Integration.
If the two compared molecules have a different number of atoms (e.g
Theophylline and Methylxanithe) what should I do in order to simulate it well
(it's written that you have to have the same number of atoms)?
Th
Dear GMCS users
Hi. Does anyone know if MD at 2K is feasible?
Thanks,
Best regards,
Asaf
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Erik Marklund [er...@xray.bmc.uu.se]
Sent: Wednesday, March 28, 2012 10:37 PM
To: Discuss
-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Asaf Farhi [asaf.fa...@weizmann.ac.il]
Sent: Thursday, March 22, 2012 6:00 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] Editing the functions of amber
Thank you very much.
Have a nice weekend,
: [gmx-users] Editing the functions of amber
On 23/03/2012 2:56 AM, Asaf Farhi wrote:
> Thank you very much for the reply.
> I tried to send this question few days ago and they said that I'm not allowed
> to post there.
> (The edition of the replica exchange shouldn't be compl
/2012 1:59 AM, Asaf Farhi wrote:
> Dear Matt
>
> Thank you very much for the reply.
> About 1 - it's cutoff in the energy, meaning that from a certain energy you
> will get this energy.
> Can this be done with the table lookups?
Yes, any potential that is a function of distan
Asaf
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Mark Abraham [mark.abra...@anu.edu.au]
Sent: Thursday, March 22, 2012 4:24 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Editing the functions of amber
On 23/03/2012 12:50 AM, Asaf Farhi
almost as formidable a task as
implementing an algorithm from scratch based on the original papers.
That said, our group has had success with modifying GROMACS code in
the past, and it turned out to be an efficient solution.
Cheers,
Matt Zwier
On Tue, Mar 20, 2012 at 11:52 AM, Asaf Farhi wrote:
Dear Gromacs User
Hi.
My name is Asaf and I'm trying to edit one of the functions in amber in order
to use it in GROMACS.
I wanted to ask if anyone knows how to do it?
Thanks in advance,
Best regards,
Asaf
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listi
Dear Gromacs user
Hi. My name is Asaf and I'm trying to edit potential parameters for the non
bonded interaction potential terms between specific atoms (k1 for 1 subset of
pairs and k2 for anoother subset of pairs).
Is the pairs section in the topology file the correct place to do this? and if
Dear gmx user
If I may I have a specific question about replica exchange.
I want to define different Hamiltonians for the different temperatures.
It seems that the replica exchange can handle it. I wanted to ask if it's
implemented in a general way so different Hamiltonians can be used for
diff
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