yourindexfile.ndx -f
yourparams.mdp
Mark
Acoot
- Original Message -
From: Mark Abraham
To: Discussion list for GROMACS users
Cc:
Sent: Monday, 27 August 2012 8:00 PM
Subject: Re: [gmx-users] GROMACS command for energy calculation
On 27/08/2012 7:42 PM, Acoot Brett wrote:
Dear Justin
On 8/27/12 6:32 AM, Acoot Brett wrote:
Hi Mark,
Then MAP file has the ability to recognize the groups saved in the index file,
which is in the same folder as the MDP file?
Any group specified in the .mdp file must be recognized by grompp (in the case
of default groups) or otherwise suppli
Original Message -
> From: Justin Lemkul
> To: Acoot Brett ; Discussion list for GROMACS users
>
> Cc:
> Sent: Monday, 27 August 2012 9:53 AM
> Subject: Re: [gmx-users] GROMACS command for energy calculation
>
>
>
> On 8/26/12 7:44 PM, Acoot Brett wrote:
>&
GROMACS users
Cc:
Sent: Monday, 27 August 2012 9:53 AM
Subject: Re: [gmx-users] GROMACS command for energy calculation
On 8/26/12 7:44 PM, Acoot Brett wrote:
Dear All,
I am still confused and I hope I can get some detailed explaination. For
example, I want to determine the interaction energy
-
From: Justin Lemkul
To: Acoot Brett ; Discussion list for GROMACS users
Cc:
Sent: Monday, 27 August 2012 9:53 AM
Subject: Re: [gmx-users] GROMACS command for energy calculation
On 8/26/12 7:44 PM, Acoot Brett wrote:
> Dear All,
>
> I am still confused and I hope I can get some
On 8/26/12 7:44 PM, Acoot Brett wrote:
Dear All,
I am still confused and I hope I can get some detailed explaination. For
example, I want to determine the interaction energy between residue 52 and
residue 105, how should I set energyggryp and what is the related commands?
And if I want to d
and
> for excluding interactions within frozen groups.
>
>
> - Original Message -
> From: Justin Lemkul
> To: Acoot Brett ; Discussion list for GROMACS users
>
> Cc:
> Sent: Monday, 27 August 2012 7:09 AM
> Subject: Re: [gmx-users] GROMACS command for energy calculation
>
for GROMACS users
Cc:
Sent: Monday, 27 August 2012 7:09 AM
Subject: Re: [gmx-users] GROMACS command for energy calculation
On 8/26/12 5:02 PM, Acoot Brett wrote:
Dear All,
After the production MD has been done, does GROMACS has a command which can
calculate the interaction energy between any
cluding interactions within frozen groups.
- Original Message -
From: Justin Lemkul
To: Acoot Brett ; Discussion list for GROMACS users
Cc:
Sent: Monday, 27 August 2012 7:09 AM
Subject: Re: [gmx-users] GROMACS command for energy calculation
On 8/26/12 5:02 PM, Acoot Brett wrote:
speeding up energy calculations with mdrun -rerun and for
excluding interactions within frozen groups.
- Original Message -
From: Justin Lemkul
To: Acoot Brett ; Discussion list for GROMACS users
Cc:
Sent: Monday, 27 August 2012 7:09 AM
Subject: Re: [gmx-users] GROMACS command for
On 8/26/12 5:02 PM, Acoot Brett wrote:
Dear All,
After the production MD has been done, does GROMACS has a command which can
calculate the interaction energy between any 2 residues in a frame of structure
from the MD?
Assuming you have made proper use of energygrps in the .mdp file, you c
Dear All,
After the production MD has been done, does GROMACS has a command which can
calculate the interaction energy between any 2 residues in a frame of structure
from the MD?
Cheers,
Acoot
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