Re: [gmx-users] InflateGRO methodology deletion radius

. Those are really kind of you. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, June 15, 2013 4:18 PM Subject: Re: [gmx-users] InflateGRO

Re: [gmx-users] InflateGRO methodology deletion radius

, June 19, 2013 3:45 PM Subject: Re: [gmx-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

Re: [gmx-users] InflateGRO methodology deletion radius

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

Re: [gmx-users] InflateGRO methodology deletion radius

Subject: Re: [gmx-users] InflateGRO methodology deletion radius 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

[gmx-users] InflateGRO methodology deletion radius

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

Re: [gmx-users] InflateGRO methodology deletion radius

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