st 21, 2012 6:00 PM
Subject: Re: [gmx-users] EM in kalp15_DPPC
On 8/21/12 9:24 AM, Shima Arasteh wrote:
>
>
> To remove the periodicity I ran the command trjconv -s em.tpr -f
>dppc128.gro -o dppc128_whole.gro -pbc mol -ur compact and chose "system" .
> Is removing the pe
To: Discussion list for GROMACS users
Cc:
Sent: Tuesday, August 21, 2012 5:00 PM
Subject: Re: [gmx-users] EM in kalp15_DPPC
On 8/21/12 8:01 AM, Shima Arasteh wrote:
Thanks for your reply.
In order to check the warning of grompp after scaling up I ran grompp again
without -maxwarn
om the begining!
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Discussion list for GROMACS users
Cc:
Sent: Tuesday, August 21, 2012 5:00 PM
Subject: Re: [gmx-users] EM in kalp15_DPPC
On 8/21/12 8:01 AM, Shima Arasteh wrote:
>
>
> Thanks for your reply.
On 8/21/12 8:01 AM, Shima Arasteh wrote:
Thanks for your reply.
In order to check the warning of grompp after scaling up I ran grompp again
without -maxwarn:
grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr
WARNING 1 [file minim.mdp]:
The sum of the two largest charge
2012 3:09 PM
Subject: Re: [gmx-users] EM in kalp15_DPPC
On 8/21/12 6:35 AM, Shima Arasteh wrote:
> Allright, I will check the configurations of out and inputs to find out the
> reason of warning.
> Please let me know something:
> Should I expect to see changes in area per lipids in
On 8/21/12 6:35 AM, Shima Arasteh wrote:
Allright, I will check the configurations of out and inputs to find out the
reason of warning.
Please let me know something:
Should I expect to see changes in area per lipids in each shrinking or it would
happen after 25th repeat suddenly?
It will d
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
Sent: Tuesday, August 21, 2012 2:57 PM
Subject: Re: [gmx-users] EM in kalp15_DPPC
On 8/21/12 6:14 AM, Shima Arasteh wrote:
>
>
>
> Hi,
>
> I'm doing the KALP-15 IN DPPC through the Ju
On 8/21/12 6:14 AM, Shima Arasteh wrote:
Hi,
I'm doing the KALP-15 IN DPPC through the Justin's tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
The problem I got stuck into, is in "2. Pack the lipids around the protein"
step
Hi,
I'm doing the KALP-15 IN DPPC through the Justin's tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
The problem I got stuck into, is in "2. Pack the lipids around the protein"
step.
After generating the new position restrain
9 matches
Mail list logo
