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
--
gmx-user
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 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 solvent and
Thank you very much from your time.
Best Regards
Sara
- Original Message -
From: Mark Abraham
To: Discussion list for GROMACS users
Cc:
Sent: Friday, October 5, 2012 9:48 AM
Subject: Re: [gmx-users] equilibrium for box of simulation
On 5/10/2012 4:12 PM, mohammad agha wrote
- Original Message -
From: Mark Abraham
To: Discussion list for GROMACS users
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, decreasing of box dimensions is n
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 of in the most o
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 equilibr
didn't see the report of decreasing of box dimensions!
May I know your idea about it, Please?
Best Regards
Sara
- Original Message -
From: Justin Lemkul
To: mohammad agha ; Discussion list for GROMACS users
Cc:
Sent: Thursday, October 4, 2012 7:57 PM
Subject: Re: [gmx-users]
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: d=m
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 Messa
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 wi
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 with
> 6
istake and it is natural?
Best Regards
Sara
- Forwarded Message -
From: Justin Lemkul
To: mohammad agha ; Discussion list for GROMACS users
Cc:
Sent: Thursday, October 4, 2012 5:52 PM
Subject: Re: [gmx-users] equilibrium for box of simulation
On 10/4/12 10:06 AM, mohammad agha wro
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, the
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, the
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 pressu
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 try
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 s
Dear Gromacs Users,
I have a system consists of cyclohexan, pentanol, surfactant and water
in MARTINI coarse-grained ff, when I do pr.mdp for this system
(posre.itp file is only for surfactant), water molecules are not
distributed and are aggregated in one place in the box.
I don't know what shoul
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