ednesday, November 6, 2013 11:22:09 AM
Subject: Re: [gmx-users] stopped simulation
On 11/6/13 2:14 PM, Ehsan Sadeghi wrote:
> Many thanks Justin. What is an appropriate cut-off value? My box size is d=
> 0.5 nm; based on the definition of cut-off radius, its value shouble be
> smaller t
"
To: "Discussion list for GROMACS users"
Sent: Wednesday, November 6, 2013 10:54:42 AM
Subject: Re: [gmx-users] stopped simulation
On 11/6/13 12:53 PM, Ehsan Sadeghi wrote:
> Hi gmx users,
>
> I have simulated ionomer in water solution using gromos force field. But in
Hi gmx users,
I have simulated ionomer in water solution using gromos force field. But in
middle of simulation(after 2 ns) the simulation stopped and I received these
messages:
WARNING: Listed nonbonded interaction between particles 174 and 188
at distance 3f which is larger than the table lim
Hi gmx users,
I want to simulate ionomer is mixed solution of water and ethanol using gromos
force field.
I tired to follow the steps suggested on gromacs website, which are:
1- Determine the number of co-solvent molecules necessary, given the box
dimensions of your system.
2- Generate a
From: "Justin Lemkul"
To: "Discussion list for GROMACS users"
Sent: Thursday, October 31, 2013 1:18:07 PM
Subject: Re: [gmx-users] problem vwith ethanol-water solution
On 10/31/13 2:25 PM, Ehsan Sadeghi wrote:
> Hi gmx users,
>
> I want to solvate nafion molecules
Hi gmx users,
I want to solvate nafion molecules in a 3:1 ethanol water solution. I used
genbox with -ci option to add ethanol to water when generating the box, but it
did not work. Then, first I solvated the ethanol in water, and then added the
nafion to the system, but these 3 molecules each
Hi Kevin,
It seems interesting. I would like to try it out. May I have an account?
Best regards,
Ehsan
- Original Message -
From: "Kevin Chen"
To: "Discussion list for GROMACS users"
Sent: Tuesday, October 22, 2013 7:34:10 AM
Subject: [gmx-users] a new GROMACS simulation tool
Hi Eve
- Original Message -
From: "Justin Lemkul"
To: "Discussion list for GROMACS users"
Sent: Friday, October 11, 2013 9:44:33 AM
Subject: Re: [gmx-users] bonded interactions in Gromos96
On 10/11/13 12:40 PM, Ehsan Sadeghi wrote:
> Hi gromacs users,
>
> I tried to add n
Hi gromacs users,
I tried to add new bonded interactions to the ffbonded.itp file in gromos96,
but I am confused about the used parameters in the descriptions. Here is an
example:
#define gb_10.1000 1.5700e+07
; H - OA 750
The equation used in gromos is Vb(r_ij)=(1/4) k_ij (
t: Thursday, October 3, 2013 1:09:05 PM
Subject: Re: [gmx-users] double bond
On 10/3/13 3:08 PM, Ehsan Sadeghi wrote:
> Hi gromacs users,
>
> In my nafion sidechain, I have -CF2-SO3H. In this molecule, S atom has 2
> double bonds with 2 O, 1 single bond with another O, and i sing
Hi gromacs users,
In my nafion sidechain, I have -CF2-SO3H. In this molecule, S atom has 2 double
bonds with 2 O, 1 single bond with another O, and i single bond with C (total 6
bonds). When I do energy minimization in vacuum, I got two F atoms nonbonded to
my C atom. I think, gromacs generate
edral? I received 89 errors for not
defining them.
Kind regards,
Ehsan
- Original Message -
From: "Justin Lemkul"
To: "Discussion list for GROMACS users"
Sent: Monday, September 30, 2013 11:27:25 AM
Subject: Re: [gmx-users] ionomer topolgy
On 9/30/13 2:23 PM, Ehsan
ist for GROMACS users"
Sent: Monday, September 30, 2013 1:45:41 PM
Subject: Re: [gmx-users] ionomer topolgy
On 9/30/13 4:40 PM, Ehsan Sadeghi wrote:
> Many thanks Justin.
>
> Apparently I was modifying the .rtp file in the wrong location; now the
> pdb2gmx works and I can start
; Subject: Re: [gmx-users] ionomer topolgy
>
>
>
> On 9/30/13 12:50 PM, Ehsan Sadeghi wrote:
>> Thanks Justin,
>>
>> I modified the pdb file, but it cannot recognize my residue LIG. Here is the
>> error:
>>
>> Opening force field file
>> /usr/l
ject: Re: [gmx-users] ionomer topolgy
On 9/30/13 12:50 PM, Ehsan Sadeghi wrote:
> Thanks Justin,
>
> I modified the pdb file, but it cannot recognize my residue LIG. Here is the
> error:
>
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/amino
sers] ionomer topolgy
On 9/27/13 8:43 PM, Ehsan Sadeghi wrote:
> Thanks for your prompt response. I made the modifications on the
> aminoacids.rtp file in Gromacs/gromacs-4.6.3/share/top/gromos53a6.ff.
>
> I did not modify any force field. I thought I still can use the default fo
13 3:06:05 PM
Subject: Re: [gmx-users] ionomer topolgy
On 9/27/13 5:53 PM, Ehsan Sadeghi wrote:
> Hello,
>
> I revised my pdb and rtp files. I still receive similar error message.
>
Whatever modifications you're making probably aren't being done in the right
files. You
: "Justin Lemkul"
To: "Discussion list for GROMACS users"
Sent: Friday, September 27, 2013 1:24:44 PM
Subject: Re: [gmx-users] ionomer topolgy
On 9/27/13 4:18 PM, Ehsan Sadeghi wrote:
> Hi,
>
> I just added this to the existing .rtp file in gromos
>
> [ LIG ]
&g
Thanks Justin.
I try to modify my file based on your comments.
- Original Message -
From: "Justin Lemkul"
To: "Discussion list for GROMACS users"
Sent: Friday, September 27, 2013 1:24:44 PM
Subject: Re: [gmx-users] ionomer topolgy
On 9/27/13 4:18 PM, Ehsan Sadegh
H 0.000 0
I also added LIG and SCH to the residuetypes.dat
Kind regards,
Ehsan
- Original Message -
From: "Justin Lemkul"
To: "Discussion list for GROMACS users"
Sent: Friday, September 27, 2013 12:29:38 PM
Subject: Re: [gmx-users] ionomer topolgy
On 9/
he GROMACS
Thank you,
Ehsan
- Original Message -
From: "Justin Lemkul"
To: "Discussion list for GROMACS users"
Sent: Friday, September 27, 2013 11:50:13 AM
Subject: Re: [gmx-users] ionomer topolgy
On 9/27/13 2:34 PM, Ehsan Sadeghi wrote:
> Hello Gromacs users,
&g
Hello Gromacs users,
I am the beginner in Gromacs. I want to simulate ionomer in water. I could not
find a pdb file for my case, and I tried to draw the ionomer in Avogadro
software and generated the pdb file. However, gmx cannot find my residue names.
I added my residue name to residuetypes.da
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