Thanks for the explanation and the suggestions. The values I mentioned in the
last mail were obtained when using tau_p = 2. I have tried changing tau_p in the
mdp file to 0.8 and 1.0. With tau_p = 1.0 the average pressure is around 0.9 but
with tau_p = 0.8 the pressure is ~ -0.3 (time = 10ns). Is t
On 7/26/13 4:06 PM, Quintin Sheridan wrote:
Dear Gromacs Users,
Is it possible to run free energy calculations in parallel using mpirun? If
Yes, the free energy code is parallelized, either via MPI or threads.
not I am wondering what the fastest way to run a free energy calculation
is. I a
On 7/26/13 12:37 PM, Davit Hakobyan wrote:
Date: Fri, 26 Jul 2013 11:30:14 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Calculate interaction energy dynamically
On 7/26/13 5:21 AM, Davit Hakobyan wrote:
From: davhak2...@hotmail.com
To: gmx-users@gromacs.
Dear Gromacs Users,
Is it possible to run free energy calculations in parallel using mpirun?
If not, what is the fastest way to run free energy calculations. I am
trying to us the Bennet's Accepetance Ratio (g_bar) to get the free energy
of solvation for an ionic liquid based on the tutorial by
Dear Gromacs Users,
Is it possible to run free energy calculations in parallel using mpirun? If
not I am wondering what the fastest way to run a free energy calculation
is. I am basing my free energy calculation on the tutorial by Justin Lemkul
found at
http://www.bevanlab.biochem.vt.edu/Pages/Pe
Alright, I think I have enough information now to play around with some
settings!
Thank you very much Justin, you have been very helpful :)
-Jonathan
--
View this message in context:
http://gromacs.5086.x6.nabble.com/Limitations-of-simulations-tp5010100p5010147.html
Sent from the GROMACS User
> Date: Fri, 26 Jul 2013 11:30:14 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Calculate interaction energy dynamically
>
>
>
> On 7/26/13 5:21 AM, Davit Hakobyan wrote:
> >> From: davhak2...@hotmail.com
> >> To: gmx-users@gromacs.org
> >> Subject: RE: [
Please remember to keep the discussion on the list.
On 7/26/13 12:04 PM, Shima Arasteh wrote:
what I aim to see is that the pulled ion should be remained in center of the
channel (peptide inserted in lipid bilayer).
I didn't restrain the channel, it makes a little bit hard for me to judge
exa
On 7/26/13 11:52 AM, Shima Arasteh wrote:
Thanks for your previous replies. All are always beneficial and I appreciate
you.
As I see in pullx.xvg file, the third column refers to the distance of pull
group and reference group. All around -1.2. Is it sufficient to judge that the
US has bee
Thanks for your previous replies. All are always beneficial and I appreciate
you.
As I see in pullx.xvg file, the third column refers to the distance of pull
group and reference group. All around -1.2. Is it sufficient to judge that the
US has been performed properly?
Thanks for your suggest
On 7/26/13 5:21 AM, Davit Hakobyan wrote:
From: davhak2...@hotmail.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] Calculate interaction energy dynamically
Date: Thu, 25 Jul 2013 09:13:14 +
Date: Wed, 24 Jul 2013 09:35:26 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subj
Dear gmx-users list members-
I'd like to remind you all about the 2013 GROMACS Workshop and
Conference at the University of Virginia Sept 13th-15th; registration
costs will rise from $60 to $95 on Aug 22nd. The original invitation,
with link to the website, is at the end of this email.
We are iss
Hi Anna,
On Jul 26, 2013, at 11:17 AM, battis...@libero.it wrote:
> Dear Carsten,
>
> thank you very much for your support!
>
> At the beginning I did not follow your indications correctly but now, using
> the orientation restraints and the indication in the paper
I think you do not need orien
> From: davhak2...@hotmail.com
> To: gmx-users@gromacs.org
> Subject: RE: [gmx-users] Calculate interaction energy dynamically
> Date: Thu, 25 Jul 2013 09:13:14 +
>
>
>
> > Date: Wed, 24 Jul 2013 09:35:26 -0400
> > From: jalem...@vt.edu
> > To: gmx-users@gromacs.org
> > Subject: Re: [gmx-use
Dear Carsten,
thank you very much for your support!
At the beginning I did not follow your indications correctly but now, using
the orientation restraints and the indication in the paper
Keep it Flexible: Driving Macromolecular Rotary Motions in Atomistic
Simulations with GROMACS
Kutzner C, Cz
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