Re: [gmx-users] Umbrella Sampling settings

2013-07-12 Thread Shima Arasteh
[gmx-users] Umbrella Sampling settings On 7/12/13 11:32 AM, Shima Arasteh wrote: > > > > Allright. > As I said earlier, my system is a lipid bilayer. A channel is inserted in it > and I want to run US on this system. > An ion is considered in center of the each window, the rea

Re: [gmx-users] Umbrella Sampling settings

2013-07-12 Thread Justin Lemkul
On 7/12/13 11:32 AM, Shima Arasteh wrote: Allright. As I said earlier, my system is a lipid bilayer. A channel is inserted in it and I want to run US on this system. An ion is considered in center of the each window, the reaction coordinate is set to z, so the group which is pulled is an

Re: [gmx-users] Umbrella Sampling settings

2013-07-12 Thread Shima Arasteh
group? Would you please give me any suggestions? Thanks for all your time and consideration. Sincerely, Shima - Original Message - From: Justin Lemkul To: Discussion list for GROMACS users Cc: Sent: Friday, July 12, 2013 1:41 AM Subject: Re: [gmx-users] Umbrella Sampling settings On

Re: [gmx-users] Umbrella Sampling settings

2013-07-12 Thread Shima Arasteh
group? Would you please give me any suggestions? Thanks for all your time and consideration. Sincerely, Shima - Original Message - From: Justin Lemkul To: Discussion list for GROMACS users Cc: Sent: Friday, July 12, 2013 1:41 AM Subject: Re: [gmx-users] Umbrella Sampling settings On 7/

Re: [gmx-users] Umbrella Sampling settings

2013-07-11 Thread Justin Lemkul
ima - Original Message - From: Justin Lemkul To: Shima Arasteh ; Discussion list for GROMACS users Cc: Sent: Friday, July 12, 2013 1:37 AM Subject: Re: [gmx-users] Umbrella Sampling settings On 7/11/13 4:21 PM, Shima Arasteh wrote: Hi, I want to run Umbrella Sampling on m

Re: [gmx-users] Umbrella Sampling settings

2013-07-11 Thread Shima Arasteh
013 1:37 AM Subject: Re: [gmx-users] Umbrella Sampling settings On 7/11/13 4:21 PM, Shima Arasteh wrote: > Hi, > > I want to run Umbrella Sampling on my system. In initial configurations, an > ion is located in center of the window. > Some mdp file settings for running US, as I

Re: [gmx-users] Umbrella Sampling settings

2013-07-11 Thread Justin Lemkul
On 7/11/13 4:21 PM, Shima Arasteh wrote: Hi, I want to run Umbrella Sampling on my system. In initial configurations, an ion is located in center of the window. Some mdp file settings for running US, as I found in US tutorial are : ; Pull code pull= umbrella pull_geometry = dist

[gmx-users] Umbrella Sampling settings

2013-07-11 Thread Shima Arasteh
Hi, I want to run Umbrella Sampling on my system. In initial configurations, an ion is located in center of the window. Some mdp file settings for running US, as I found in US tutorial are : ; Pull code pull    = umbrella pull_geometry   = distance pull_dim    = N N Y pull_start