Re: Aw: [gmx-users] unable to equilibrate pressure in npt

2013-07-26 Thread amin
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

Re: [gmx-users] Free Energy Calculations in Parallel

2013-07-26 Thread Justin Lemkul
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

Re: [gmx-users] Calculate interaction energy dynamically

2013-07-26 Thread Justin Lemkul
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.

[gmx-users] Free Energy Simulations in Parallel

2013-07-26 Thread Quintin Sheridan
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

[gmx-users] Free Energy Calculations in Parallel

2013-07-26 Thread Quintin Sheridan
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

[gmx-users] Re: Limitations of simulations?

2013-07-26 Thread Jonathan Saboury
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

RE: [gmx-users] Calculate interaction energy dynamically

2013-07-26 Thread Davit Hakobyan
> 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: [

Re: Fw: [gmx-users] Umbrella Sampling _ pulled ion

2013-07-26 Thread Justin Lemkul
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

Re: Fw: [gmx-users] Umbrella Sampling _ pulled ion

2013-07-26 Thread Justin Lemkul
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

Fw: [gmx-users] Umbrella Sampling _ pulled ion

2013-07-26 Thread Shima Arasteh
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

Re: [gmx-users] Calculate interaction energy dynamically

2013-07-26 Thread Justin Lemkul
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

[gmx-users] Reminder about US GROMACS workshop + soliciting presenters for talks and tutorials

2013-07-26 Thread Michael Shirts
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

Re: [gmx-users] Rotation Constraints - PMF - external potential

2013-07-26 Thread Carsten Kutzner
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

RE: [gmx-users] Calculate interaction energy dynamically

2013-07-26 Thread Davit Hakobyan
> 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

R: Re: [gmx-users] Rotation Constraints - PMF - external potential

2013-07-26 Thread battis...@libero.it
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