Thanks alot I did solve visualization problem using trjconv. Is it o.k. to use Berendsen thermostat for thermal unfolding of protein. I came across literature saying Berendsen coupling does not gives accurate kinetic Energy. I am using it and I am getting my protein unfolded. Am I right. Can I use the trajectory obtained for thermodynamic analysis. Thanks in advance msnayeem
On 4/3/10, Justin A. Lemkul <[email protected]> wrote: > > > > shahid nayeem wrote: > >> Dear All >> I am working on protein unfolding >> simulation in gromacs. when I do a production run on 32 node HPC I get >> .trr file along with .gro. when I try to visualize this files in >> VMD I see erratic large movement of atoms in the trajectory. With same >> .mdp files when I did smaller run of 2ns on single PC and viewed .trr >> and .gro in VMD, the movemnt of atom was smooth. Why this is >> happening. When I used the command g_filter to produce lowpass.xtc >> > > This sounds like a consequence of periodic boundary conditions. Have you > tried using trjconv to fix the PBC effects (i.e., -pbc mol, -pbc nojump, or > something similar)? > > with -nf 10 I got the smooth movement of atoms. Is it always essential >> to use g_filter with .trr file of HPC multinode output. what is the >> difference between lowpass.xtc and highpass.xtc. For the pupose of >> > > The purpose is to smooth out high-frequency vibration to make visualization > a bit easier and movie-rendering more meaningful. See g_filter -h for the > difference between the two; they are explained quite thoroughly. > > RMSD calculation should I use the output of g_filter i.e. lowpass.xtc >> or the original .trr file. I am new in this field so excuse me for >> > > Use the original (PBC-corrected) trajectory. > > -Justin > > some basic mistakes . Any suggestion and help will highly appreciated. >> Thanking you in advance. >> msnayeem >> >> [email protected] >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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 >
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