Hi Hazizian, > I have done md simulation of a 2-domain protein in water, > in 50 K but every > time I did it these domains are separated from each other, > and dont correct > when I do trjconv -pbc nojump,
This also happened to me once, since it can be impossible to correct the trajectory with nojump once the protein goes through the periodic boundaries. If I recall right, the solution was to use 'comm_mode' and 'comm_grps' in the *.mdp file to ensure that the protein stays in the middle of the cell and does not cross a boundary. Hope that helped, Vaclav --- On Sun, 10/18/09, hazizian <[email protected]> wrote: > From: hazizian <[email protected]> > Subject: [gmx-users] protein domain separation > To: [email protected] > Date: Sunday, October 18, 2009, 7:38 AM > > Hi > I have done md simulation of a 2-domain protein in water, > in 50 K but every > time I did it these domains are separated from each other, > and dont correct > when I do trjconv -pbc nojump, > previous time when I did em or pr by doing trjconv -pbc > nojump, it > corrected. > > The 50.mdp file is: > title > = n.pdb > cpp > = /lib/cpp > constraints = > none > integrator = md > dt > = 0.001 > nsteps > = 100000 > constraint_algorithm = shake > shake_tol = > 0.0001 > nstcomm > = 1 > comm_mode > = Angular > nstxout > = 250 > nstvout > = 1000 > nstfout > = 0 > nstlog > = 10 > nstenergy > = 10 > nstlist > = 10 > ns_type > = grid > rlist > = 1.2 > coulombtype = > PME > rcoulomb = > 1.2 > rvdw > = 1.4 > fourierspacing = 0.12 > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > pme_order > = 4 > ewald_rtol = 1e-5 > optimize_fft = yes > > > > ; Berendsen temperature coupling is on in three groups > Tcoupl > = berendsen > tau_t > = 0.4 > 0.4 > tc-grps > = protein non-protein > > ref_t > = 50 > 50 > ; Pressure coupling is on > Pcoupl > = berendsen > tau_p > = 2 > compressibility = 4.5e-5 > ref_p > = 1.0 > ; Generate velocites is on at 50 K. > gen_vel > = yes > gen_temp = > 50.0 > gen_seed = > 173529 > > are they realy separated or I should do a command to > correct it, I search in > mailing list and could not find the result, please guide > me, thank you in > advance. > > -- > Tehran University of Medical Sciences > www.tums.ac.ir > > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > _______________________________________________ > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use > the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
