Re: [gmx-users] protein domain separate

2009-10-18 Thread Tsjerk Wassenaar
Hi, You have to use -pbc nojump with a _suitable_ reference. Cheers, Tsjerk On Sun, Oct 18, 2009 at 11:59 AM, hazizian wrote: > Hi again > I use -pbc mol -ur compact but the problem still exist. > > > -- > Tehran University of Medical Sciences > www.tums.ac.ir > > > -- > This message has been

Re: [gmx-users] protein domain separate

2009-10-17 Thread David van der Spoel
hazizian wrote: Hi As I told in my perevious mail, My system consist of a 2-domain protein (Domain A and B), even when I did EM minimization this 2 damain separated. No they didn't. Check the website. my em.mpf is: title = n.pdb cpp = /lib/cpp define

Re: [gmx-users] protein domain separate

2009-10-13 Thread Mark Abraham
hazizian wrote: Hi I want to do MD on a two-domain protein (Protein A, Protein B). After doning position restranit for 20 ps, the final structure separated. How could I keep these 2 domain close to each other during whole MD run. Check that they're not separated because of a PBC artefact (try