On 6/19/13 7:23 AM, Shima Arasteh wrote:
Do you mean another published paper rather than published one in Methods
Journal? Another one which explains the algorithm?
That's a useful one. There is a lot of helpful information on the InflateGRO
website (http://www.csb.bit.uni-bonn.de/inflate
-users] InflateGRO methodology deletion radius
On 6/19/13 12:39 AM, Shima Arasteh wrote:
> Do you mean the commands of inflateGRO controls the deletion radius?
>
Yes, that's its purpose. There is a published paper about its algorithm; I
would suggest you read and understand i
in advance. Those are really kind of you.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Saturday, June 15, 2013 4:18 PM
Subject: Re: [gmx-users] InflateGRO methodology deletion radius
On 6/15/13 3:56 AM, Shima Ara
for your suggestions in advance. Those are really kind of you.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Saturday, June 15, 2013 4:18 PM
Subject: Re: [gmx-users] InflateGRO methodology deletion radius
On
On 6/15/13 3:56 AM, Shima Arasteh wrote:
Hi,
In Kalp15_DPPC tutorial, when the InflateGRO methodology is applied to pack the
lipids, I need to follow the iteration while the cutoff value changed to 0.
I' d like to know what settings of EM.mdp file are suggested to get the best
results of doi
Hi,
In Kalp15_DPPC tutorial, when the InflateGRO methodology is applied to pack the
lipids, I need to follow the iteration while the cutoff value changed to 0.
I' d like to know what settings of EM.mdp file are suggested to get the best
results of doing shrinking steps?
When I set the settings a
I don't know! :))
Sincerely,
Shima
- Original Message -
From: Peter C. Lai
To: Discussion list for GROMACS users
Cc:
Sent: Sunday, September 23, 2012 10:52 AM
Subject: Re: [gmx-users] InflateGro methodology
Why don't you just try it and see what happens?
On 2012-09-23
Why don't you just try it and see what happens?
On 2012-09-23 12:19:20AM -0700, Shima Arasteh wrote:
>
>
> Dear users,
>
> I wanna pack the lipids around my protein. To do so, InflateGro methodology
> is applied. Following Justin's tutorial KALP15-DPPC, the first step is
> scaling up 4 times:
Dear users,
I wanna pack the lipids around my protein. To do so, InflateGro methodology is
applied. Following Justin's tutorial KALP15-DPPC, the first step is scaling up
4 times:
# perl inflategro.pl system.gro 4 POPC 14 system-inflated.gro 5 area.dat
and then shrinking it for 26 times.
I'd
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