Re: [gmx-users] MARTINI force-field in pulling simulations

2013-02-08 Thread Davide Mercadante
Thanks Justin. The help has been much appreciated. Cheers, Davide On 7/02/13 8:46 PM, "Justin Lemkul" wrote: > > >On 2/7/13 2:29 PM, Davide Mercadante wrote: >> Thank you Justin, >> >> I guess this means that this kind of simulations is not possible >>without a >> modification of the forcefiel

Re: [gmx-users] MARTINI force-field in pulling simulations

2013-02-07 Thread Justin Lemkul
On 2/7/13 2:29 PM, Davide Mercadante wrote: Thank you Justin, I guess this means that this kind of simulations is not possible without a modification of the forcefield (which would ultimately mean using a different forcefield I believe)? If you're looking to unfold secondary structure eleme

Re: [gmx-users] MARTINI force-field in pulling simulations

2013-02-07 Thread Davide Mercadante
Thank you Justin, I guess this means that this kind of simulations is not possible without a modification of the forcefield (which would ultimately mean using a different forcefield I believe)? Thanks. Cheers, Davide On 7/02/13 8:09 PM, "Justin Lemkul" wrote: > > >On 2/7/13 1:44 PM, Davide

Re: [gmx-users] MARTINI force-field in pulling simulations

2013-02-07 Thread Justin Lemkul
On 2/7/13 1:44 PM, Davide Mercadante wrote: Dear Justin, Thank you for your reply. I decreased the time step from 0.02 to 0.005 and run the simulation again. The simulation still crashes giving LINCS warning on the same atoms but does it later. Do you advice to keep reducing the time step in o

Re: [gmx-users] MARTINI force-field in pulling simulations

2013-02-07 Thread Davide Mercadante
Dear Justin, Thank you for your reply. I decreased the time step from 0.02 to 0.005 and run the simulation again. The simulation still crashes giving LINCS warning on the same atoms but does it later. Do you advice to keep reducing the time step in order to reach a simulated time where the pull o

Re: [gmx-users] MARTINI force-field in pulling simulations

2013-02-07 Thread Justin Lemkul
On 2/7/13 5:20 AM, Davide Mercadante wrote: Dear All, I am trying to run a pulling simulation on a small protein (18 aa) using the GC forcefield MARTINI (v2.2). I have energy minimized and equilibrated (NPT) my system and everything seems fine. My system consists of the protein + water + ions

[gmx-users] MARTINI force-field in pulling simulations

2013-02-07 Thread Davide Mercadante
Dear All, I am trying to run a pulling simulation on a small protein (18 aa) using the GC forcefield MARTINI (v2.2). I have energy minimized and equilibrated (NPT) my system and everything seems fine. My system consists of the protein + water + ions NA+ and CL-. After the equilibration I start a