Re: [gmx-users] Re: free energy calculations of methane in water computed by GMX ver 4.5.7 and ver 4.6.2

2013-06-23 Thread Justin Lemkul
On 6/23/13 1:13 AM, Dwey wrote: Hi Justin, Thank you for sharing your experience with me. As suggested, Gromacs ver 4.5.5 is compiled within the same Linux box and I am able to reproduce a similar result ( DG= -9.30 kJmol-1). Gromacs ver 4.5.5 and 4.6.2 both are compiled from source co

[gmx-users] Re: free energy calculations of methane in water computed by GMX ver 4.5.7 and ver 4.6.2

2013-06-22 Thread Dwey
Hi Justin, Thank you for sharing your experience with me. As suggested, Gromacs ver 4.5.5 is compiled within the same Linux box and I am able to reproduce a similar result ( DG= -9.30 kJmol-1). Gromacs ver 4.5.5 and 4.6.2 both are compiled from source codes, while Gromacs ver 4.5.7 as repor

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

2013-06-12 Thread JW Gibbs
Thanks Justin and Professor Shirts. The gmxdump on the resulting tpr did indeed solve a lot of my problems. Thanks again. -- View this message in context: http://gromacs.5086.x6.nabble.com/Free-Energy-Calculations-in-Gromacs-tp5007495p5009115.html Sent from the GROMACS Users Forum mailing list

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

2013-06-10 Thread Michael Shirts
An important final point is that you can always see EXACTLY what grompp is putting into the B state by running gmxdump on the resulting tpr. It's a LOT of information, but all in text all the interactions are listed explicitly there. On Mon, Jun 10, 2013 at 6:20 PM, Justin Lemkul wrote: > > > On

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

2013-06-10 Thread Justin Lemkul
On 6/10/13 2:50 PM, JW Gibbs wrote: Hi, I have been trying to perform the simulations using the amber forcefield, in which the [ pairtypes ] directive is not defined explicitly in the ffnonbonded.itp file, but rather the 1-4 interactions are generated as per the defaults section in the forcefi

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

2013-06-10 Thread JW Gibbs
Hi, I have been trying to perform the simulations using the amber forcefield, in which the [ pairtypes ] directive is not defined explicitly in the ffnonbonded.itp file, but rather the 1-4 interactions are generated as per the defaults section in the forcefield.itp file. I was wondering what happe

Re: [gmx-users] Re: free energy calculations

2011-07-06 Thread Justin A. Lemkul
Ragothaman Yennamalli wrote: Message: 1 Date: Tue, 05 Jul 2011 19:14:04 -0400 From: "Justin A. Lemkul" mailto:jalem...@vt.edu>> Subject: Re: [gmx-users] free energy calculations To: Discussion list for GROMACS users mailto:gmx-users@gromacs.org>> Message-ID: <4e139abc

[gmx-users] Re: free energy calculations

2011-07-06 Thread Ragothaman Yennamalli
> > > Message: 1 > Date: Tue, 05 Jul 2011 19:14:04 -0400 > From: "Justin A. Lemkul" > Subject: Re: [gmx-users] free energy calculations > To: Discussion list for GROMACS users > Message-ID: <4e139abc.1030...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > Ragothaman

[gmx-users] Re: Free energy calculations - desolvation energy of Na+

2010-10-26 Thread eva . pluharova
Hi Justin, thanks for this link: http://lists.gromacs.org/pipermail/gmx-users/2003-June/006054.html It clearly says, why sampling by MD is not proper. Best, Eva >> Hello all, >> >> I am trying calculate desolvation free energy of Na+ in water using >> option >> couple-moltype, not by creatin