Re: [gmx-users] InflateGRO methodology deletion radius

2013-06-19 Thread Justin Lemkul
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

Re: [gmx-users] InflateGRO methodology deletion radius

2013-06-19 Thread Shima Arasteh
-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

Re: [gmx-users] InflateGRO methodology deletion radius

2013-06-19 Thread Justin Lemkul
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

Re: [gmx-users] InflateGRO methodology deletion radius

2013-06-18 Thread Shima Arasteh
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

Re: [gmx-users] InflateGRO methodology deletion radius

2013-06-15 Thread Justin Lemkul
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

[gmx-users] InflateGRO methodology deletion radius

2013-06-15 Thread Shima Arasteh
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

Re: [gmx-users] InflateGro methodology

2012-09-23 Thread Shima Arasteh
 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

Re: [gmx-users] InflateGro methodology

2012-09-23 Thread Peter C. Lai
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:

[gmx-users] InflateGro methodology

2012-09-23 Thread Shima Arasteh
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