Dear GROMACS Specialists,
We know that one system is at equilibrium state when the variation of Helmholtz
or Gibbs free energy be zero.
May I ask you say me that how I can understand that my system has reached to
equilibrium state in the end of simulation, Please?
Best Regards
Sara
--
Dear Gromacs Users,
I have one system consists of: surfactant, solvent and additives. I made one
box with only solvent and one box with only additives and equilibrated them
little separable for better placing into the box, and then made one box with
surfactant and then placed box of solvent
Dear Gromacs Users,
I have one system consists of: surfactant, solvent and additives. I made one
box with only solvent and one box with only additives and equilibrated them
little separable for better placing into the box, and then made one box with
surfactant and then placed box of
Dear Gromacs Users,
I have one system consists of: surfactant, solvent and additives. I made one
box with only solvent and one box with only additives and equilibrated them
little separable for better placing into the box, and then made one box with
surfactant and then placed box of solvent
On 5/10/2012 3:55 PM, mohammad agha wrote:
Dear Justin,
Thank you very much.
So, decreasing of box dimensions is not bad, if all thing process natural, yes?
The cause of my doubt was because of in the most of articles was said for example
we select box with dimensions 10nm that after
:
Sent: Friday, October 5, 2012 9:34 AM
Subject: Re: [gmx-users] equilibrium for box of simulation
On 5/10/2012 3:55 PM, mohammad agha wrote:
Dear Justin,
Thank you very much.
So, decreasing of box dimensions is not bad, if all thing process natural,
yes?
The cause of my doubt was because
Message -
From: Mark Abraham mark.abra...@anu.edu.au
To: Discussion list for GROMACS users gmx-users@gromacs.org
Cc:
Sent: Friday, October 5, 2012 9:34 AM
Subject: Re: [gmx-users] equilibrium for box of simulation
On 5/10/2012 3:55 PM, mohammad agha wrote:
Dear Justin,
Thank you very much.
So
Thank you very much from your time.
Best Regards
Sara
- Original Message -
From: Mark Abraham mark.abra...@anu.edu.au
To: Discussion list for GROMACS users gmx-users@gromacs.org
Cc:
Sent: Friday, October 5, 2012 9:48 AM
Subject: Re: [gmx-users] equilibrium for box of simulation
On 5
Dear GROMACS Users,
I asked this question before but I don't understand it!
I placed several materials in my box of simulation for example box with
6nm*6nm*6nm and my materials are not placed in the smaller box but when I
equilibrate my system, the box became smaller and temperature and
On 5/10/2012 12:06 AM, mohammad agha wrote:
Dear GROMACS Users,
I asked this question before but I don't understand it!
I placed several materials in my box of simulation for example box with
6nm*6nm*6nm and my materials are not placed in the smaller box but when I
equilibrate my system,
On 10/4/12 10:06 AM, mohammad agha wrote:
Dear GROMACS Users,
I asked this question before but I don't understand it!
I placed several materials in my box of simulation for example box with
6nm*6nm*6nm and my materials are not placed in the smaller box but when I
equilibrate my system,
and it is natural?
Best Regards
Sara
- Forwarded Message -
From: Justin Lemkul jalem...@vt.edu
To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users
gmx-users@gromacs.org
Cc:
Sent: Thursday, October 4, 2012 5:52 PM
Subject: Re: [gmx-users] equilibrium for box of simulation
:
Sent: Thursday, October 4, 2012 5:48 PM
Subject: Re: [gmx-users] equilibrium for box of simulation
On 5/10/2012 12:06 AM, mohammad agha wrote:
Dear GROMACS Users,
I asked this question before but I don't understand it!
I placed several materials in my box of simulation for example box
On 10/4/12 10:38 AM, mohammad agha wrote:
Dear Justin,
my materials are not placed in the smaller box means if I select box with
dimensions 5.99 nm, space is low and insufficient for my molecules! but after equilibrate
the box become small.
Please define what you mean here. You start
Dear Justin,
Thank you very much from your help.
Oh, yes, the vectors of box are downward in the first with much slope and then
the slope became milder and milder and then it become almost fix.
For checking of density, should I use from formula: d=m/v?
Best Regards
Sara
- Original
On 10/4/12 12:25 PM, mohammad agha wrote:
Dear Justin,
Thank you very much from your help.
Oh, yes, the vectors of box are downward in the first with much slope and then
the slope became milder and milder and then it become almost fix.
For checking of density, should I use from formula:
, 2012 7:57 PM
Subject: Re: [gmx-users] equilibrium for box of simulation
On 10/4/12 12:25 PM, mohammad agha wrote:
Dear Justin,
Thank you very much from your help.
Oh, yes, the vectors of box are downward in the first with much slope and
then the slope became milder and milder
Dear all,
I'm performing NVT on a system consisting a water layer, a decane layer
and a lipid layer in between those two layers. There are 40 lipids, 627
decane molecules and 8577 water molecules in total.
The EM was conducted successfully, however, when I try to run NVT on
this system, it
On 8/23/12 1:20 PM, Clare wrote:
Dear all,
I'm performing NVT on a system consisting a water layer, a decane layer and a
lipid layer in between those two layers. There are 40 lipids, 627 decane
molecules and 8577 water molecules in total.
The EM was conducted successfully, however, when I
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