Thanks for your kind reply .
Sincerely,
Shima
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Sent: Wednesday, May 2, 2012 7:02 PM
Subject: Re: [gmx-users] GROMOS87 and CHARMM27
On 5/2/12 10:30 AM, Shima Arasteh wrote:
>
> Thanks fo
st for GROMACS
users
*Sent:* Wednesday, May 2, 2012 5:34 PM
*Subject:* Re: [gmx-users] GROMOS87 and CHARMM27
On 5/2/12 12:21 AM, Shima Arasteh wrote:
>
> Dear Justin,
> I don't want to compare the forcefields results.
> Yes, Iwant to use some old information in conjunction with
> *From:* Peter C. Lai mailto:p...@uab.edu>>
> *To:* Discussion list for GROMACS users mailto:gmx-users@gromacs.org>>
> *Sent:* Monday, April 16, 2012 9:50 PM
> *Subject:* Re: [gmx-users] GROMOS87 and CHARMM27
>
> On 2012-04-16 10:14:01AM -0700, S
t; Thanks in advance,
> Shima
>
>
> *From:* Peter C. Lai
> *To:* Discussion list for GROMACS users
> *Sent:* Monday,
April 16, 2012 9:50 PM
> *Subject:* Re: [gmx-users] GROMOS87 and CHARMM27
>
> On 2012-04-16 10:14:01A
PM
Subject: Re: [gmx-users] GROMOS87 and CHARMM27
On 2012-04-16 10:14:01AM -0700, Shima Arasteh wrote:
> So, I can not use the coordinates of the output files of gromos runs. Right?
You can but you may need to rename the atoms for each residue for pdb2gmx
to w
e new force field.
-Justin
*From:* Peter C. Lai
*To:* Discussion list for GROMACS users
*Sent:* Monday, April 16, 2012 8:23 PM
*Subject:* Re: [gmx-users] GROMOS87 and CHARMM27
On 2012-04-16 08:26:00AM -0700, Shima Arasteh
gt; To: Discussion list for GROMACS users
> Sent: Monday, April 16, 2012 8:23 PM
> Subject: Re: [gmx-users] GROMOS87 and CHARMM27
>
> On 2012-04-16 08:26:00AM -0700, Shima Arasteh wrote:
> > Dear GROMACS users,
> >
> > I reproduced the results of a protein-membrane
So, I can not use the coordinates of the output files of gromos runs. Right?
From: Peter C. Lai
To: Discussion list for GROMACS users
Sent: Monday, April 16, 2012 8:23 PM
Subject: Re: [gmx-users] GROMOS87 and CHARMM27
On 2012-04-16 08:26:00AM -0700, Shima
On 2012-04-16 08:26:00AM -0700, Shima Arasteh wrote:
> Dear GROMACS users,
>
> I reproduced the results of a protein-membrane system by using force field
> GROMOSE87. This protein forms ion channel in membrane.
> Now if I wanna study the ion conduction through this channel using force
> field CH
Cheers,
Shima
*From:* Justin A. Lemkul
*To:* Discussion list for GROMACS users
*Sent:* Thursday, April 12, 2012 9:07 PM
*Subject:* Re: [gmx-users] Gromos87
Marz
012 9:07 PM
Subject: Re: [gmx-users] Gromos87
Marzinek, Jan wrote:
>
>
>
> *From:* Shima Arasteh [shima_arasteh2...@yahoo.com]
> *Sent:* Thursday, April 12, 2012 4:53 PM
> *To:* Marzinek, Jan
>
Marzinek, Jan wrote:
*From:* Shima Arasteh [shima_arasteh2...@yahoo.com]
*Sent:* Thursday, April 12, 2012 4:53 PM
*To:* Marzinek, Jan
*Subject:* Re: [gmx-users] Gromos87
Dear Jan,
I downloaded the file and put it
From: Shima Arasteh [shima_arasteh2...@yahoo.com]
Sent: Thursday, April 12, 2012 4:53 PM
To: Marzinek, Jan
Subject: Re: [gmx-users] Gromos87
Dear Jan,
I downloaded the file and put it in my working space but does not appear in my
force filed selections? How
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Shima Arasteh [shima_arasteh2...@yahoo.com]
Sent: Thursday, April 12, 2012 4:05 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] Gromos87
Dear friends,
I'd like to use g
Anthony Cruz wrote:
Hi:
How to convert gromos87 ferric iron heme l-j parameters:
4.30115e-5(kJ nm^-12 mol^-1) and 8.86909e-3(kJ nm^-6 mol^-1)
to use it in gromos96 FF?
Find the functional forms in which these parameters are applied and do
something intelligent. Then, sacrifice a goat and hop
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