Re: [gmx-users] MD with membrane protein

2011-10-03 Thread lina
On Tue, Oct 4, 2011 at 2:57 AM, elisa carli wrote: > Hi Lisa > Thank you very much for your reply. > After minimimization could I run a molecular dynamic production? > Or have I to do other sets? > Yes, after energy minimization, you need do some other sets (like NVT and NPT). Could you write me

Re: [gmx-users] MD with membrane protein

2011-10-03 Thread Justin A. Lemkul
elisa carli wrote: Hi Lisa Thank you very much for your reply. After minimimization could I run a molecular dynamic production? Or have I to do other sets? Could you write me which are the commands to execute up to MD run? http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_S

Re: [gmx-users] MD with membrane protein

2011-10-03 Thread elisa carli
Hi Lisa Thank you very much for your reply. After minimimization could I run a molecular dynamic production? Or have I to do other sets? Could you write me which are the commands to execute up to MD run? Bests 2011/9/22 lina > On Thu, Sep 22, 2011 at 11:34 AM, elisa carli wrote: > >> Dear All

Re: [gmx-users] MD with membrane protein

2011-09-21 Thread lina
On Thu, Sep 22, 2011 at 11:34 AM, elisa carli wrote: > Dear All > > I'd like to perfom a MD simulation on a membrane protein using DLPC or DPPC > system > I've downloaded the API package from this link > http://www.gromacs.org/Downloads/User_contributions/Molecule_topologies > > DPPC.zip and DLPC.