Dear Mark,
Unfortunately, my problem about box of simulation has not been solved!
My command lines are as follow:
1- genbox -ci solute.gro -nmol 150 -box 12 12 12 -o solute150.gro
2- editconf -f solute150.gro -o solute1501.gro -c -d 1.0 -bt cubic -box 13.6
13.6 13.6 -center 6.8 6.8 6.8
3-
Dear Mark,
Unfortunately, my problem about box of simulation has not been solved!
My command lines are as follow:
1- genbox -ci solute.gro -nmol 150 -box 12 12 12 -o solute150.gro
2- editconf -f solute150.gro -o solute1501.gro -c -d 1.0 -bt cubic -box 13.6
13.6 13.6 -center 6.8 6.8 6.8
3-
On 15/08/2012 10:27 PM, mohammad agha wrote:
Dear Mark,
Unfortunately, my problem about box of simulation has not been solved!
My command lines are as follow:
1- genbox -ci solute.gro -nmol 150 -box 12 12 12 -o solute150.gro
2- editconf -f solute150.gro -o solute1501.gro -c -d 1.0 -bt cubic
Dear Mark,
Thank you very much from your help.
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: Wednesday, August 15, 2012 5:23 PM
Subject: Re: [gmx-users] box of simulation
On 15
Dear Gromacs Users:
When I want to place 12000 solvent molecule in the box (15*15*15) it say:
number of coordinates in coordinate file (ctacyc.gro, 28794)
does not match topology (topol.top, 37950)
it means that I should enlarge the box to place all of solvent molecules into
that.
Dear Gromacs Users:
When I want to place 12000 solvent molecule in the box (15*15*15) it say:
number of coordinates in coordinate file (ctacyc.gro, 28794)
does not match topology (topol.top, 37950)
it means that I should enlarge the box to place all of solvent molecules into
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of mohammad agha
Sent: Tuesday, 14 August 2012 5:27 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] box of simulation
Dear Gromacs Users:
When I want to place 12000
@gromacs.org
Cc:
Sent: Tuesday, August 14, 2012 12:06 PM
Subject: RE: [gmx-users] box of simulation
Hi Sara,
The number of molecules in your .gro file and .top file should be the same.
That means when you want to add 12000 solvent molecules, change the number of
solvent molecules in your topology file
On 14/08/2012 5:27 PM, mohammad agha wrote:
Dear Gromacs Users:
When I want to place 12000 solvent molecule in the box (15*15*15) it say:
What's it? genbox? grompp? You can't be helped effectively if you
don't provide your command lines that produce output, and/or a
description of
...@gromacs.org] On
Behalf Of mohammad agha
Sent: Tuesday, 14 August 2012 6:08 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] Fw: box of simulation
Hi Emanuel,
Thank you very much from your response.
yes, my topology is correct.
It means that it isn't one problem
, 2012 1:01 PM
Subject: Re: [gmx-users] Fw: box of simulation
On 14/08/2012 6:16 PM, Emanuel Birru wrote:
I am not sure whether a pressure coupling equilibration enlarges the
specified box size of the simulation :)
It can.
if the box size is not appropriate to maintain the pressure coupling
On 14/08/2012 6:55 PM, mohammad agha wrote:
Dear Mark,
Thank you very much from your help.
I used from genbox to place solvent molecules. my question is : In the NPT
ensemble, for equilibrium, may the box become smaller than definite sizes
before equilibrium(for example 2nm become smaller)
Dear Mark,
Thank you very much from your help.
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: Tuesday, August 14, 2012 2:44 PM
Subject: Re: [gmx-users] box of simulation
On 14/08
13 matches
Mail list logo
