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
> 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
> >>
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
> 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-
> Date: Wed, 24 Jul 2013 09:35:26 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Calculate interaction energy dynamically
>
>
>
> On 7/24/13 9:25 AM, Davit Hakobyan wrote:
> > Thank you again for your time and help.
>
On 7/24/13 9:25 AM, Davit Hakobyan wrote:
Thank you again for your time and help.
Performing "rerun" on the original system passes without warnings with the
following output:
-
s is the case may one still
rely on the numbers obtained by g_energy for the coulomb and vdw terms
(despite the warning messages) ?
Thanks a lot for all the suggestions.
> Date: Wed, 24 Jul 2013 07:12:54 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-use
36
Date: Tue, 23 Jul 2013 17:07:09 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Calculate interaction energy dynamically
On 7/23/13 1:54 PM, Davit Hakobyan wrote:
Thank you very much for your continuous support.
Date: Tue, 23 Jul 2013 12:06:57 -0400
ate: Tue, 23 Jul 2013 17:07:09 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Calculate interaction energy dynamically
>
>
>
> On 7/23/13 1:54 PM, Davit Hakobyan wrote:
> > Thank you very much for your continuous support.
> >
On 7/23/13 1:54 PM, Davit Hakobyan wrote:
Thank you very much for your continuous support.
Date: Tue, 23 Jul 2013 12:06:57 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Calculate interaction energy dynamically
On 7/23/13 11:05 AM, Davit Hakobyan wrote
Thank you very much for your continuous support.
> Date: Tue, 23 Jul 2013 12:06:57 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Calculate interaction energy dynamically
>
>
>
> On 7/23/13 11:05 AM, Davit Hakobyan wrote:
&g
On 7/23/13 11:05 AM, Davit Hakobyan wrote:
Thanks so much for the suggestion.
By using the command:
trjorder -f system.trr -s system.tpr -n system.ndx -da 3 -na 12 -r 2.0 -o
system_ordered.trr
the resulting system_ordered.trr indeed contained lipids 2,3,4... in the
closest proximity to lip
Mon, 22 Jul 2013 08:39:27 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Calculate interaction energy dynamically
>
>
>
> On 7/22/13 8:37 AM, Davit Hakobyan wrote:
> > Thanks very much for all your suggestions!
> >
> >&
On 7/22/13 8:37 AM, Davit Hakobyan wrote:
Thanks very much for all your suggestions!
One way that you might approach it is to use mdrun -rerun. You could order the
lipids with respect to the lipid of interest, such that the reference lipid is
always molecule N and the nearest lipid is always
8:04:27 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Calculate interaction energy dynamically
>
>
>
> On 7/22/13 6:20 AM, Davit Hakobyan wrote:
> > Dear Gromacs Users,
> >
> > Is there a way in Gromacs to calculate the i
On 7/22/13 6:20 AM, Davit Hakobyan wrote:
Dear Gromacs Users,
Is there a way in Gromacs to calculate the interaction energy between any two
neighbor lipids dynamically? Since the neighbor lipids change over time in the
trajectory file specifying a static energy groups in the input script wil
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