Re: [gmx-users] Setting total simulation time
On 6/3/13 12:42 PM, Parker de Waal wrote: Thanks Mark, Using the above I ran gmxcheck -f nvt.trr Here is the resulting out put Last frame500 time 1000.000 Item#frames Timestep (ps) Step 5012 Time 5012 Lambda 5012 Coords 5012 Velocities 5012 Forces 0 Box5012 Does this mean I can interpret this as 1 ns of simulation with output every 2 ps? Yes. Also I thought when I assigned values for output at 1000, such as nstxout = 1000, that I would get an write of data every 1 ps? All of the nst* options (as the name implies and the manual explains) are given in number of steps, not time units. Thus the nst* options are dependent upon the value of dt to be given meaning in terms of time. With dt = 0.002, and nst(whatever) = 1000, you get output every 2 ps. -Justin I'm moderately confused! Parker On Mon, Jun 3, 2013 at 11:02 AM, Mark Abraham wrote: Try smaller numbers and periods for a test run, and see the machinery work. gmxcheck on the output files is your friend! Mark On Mon, Jun 3, 2013 at 4:40 PM, Parker de Waal wrote: Hi GMX-users, If I wanted to run a 1 ns simulation take snapshots every 1 ps would these be the correct input parameters? Thanks! ; Run parameters integrator = md nsteps = 50 dt = 0.002 ; Output control nstxout = 1000 nstvout = 1000 nstenergy = 1000 nstlog = 1000 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist 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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Setting total simulation time
Thanks Mark, Using the above I ran gmxcheck -f nvt.trr Here is the resulting out put Last frame500 time 1000.000 Item#frames Timestep (ps) Step 5012 Time 5012 Lambda 5012 Coords 5012 Velocities 5012 Forces 0 Box5012 Does this mean I can interpret this as 1 ns of simulation with output every 2 ps? Also I thought when I assigned values for output at 1000, such as nstxout = 1000, that I would get an write of data every 1 ps? I'm moderately confused! Parker On Mon, Jun 3, 2013 at 11:02 AM, Mark Abraham wrote: > Try smaller numbers and periods for a test run, and see the machinery work. > gmxcheck on the output files is your friend! > > Mark > > > On Mon, Jun 3, 2013 at 4:40 PM, Parker de Waal >wrote: > > > Hi GMX-users, > > > > If I wanted to run a 1 ns simulation take snapshots every 1 ps would > these > > be the correct input parameters? > > > > Thanks! > > > > ; Run parameters > > integrator = md > > nsteps = 50 > > dt = 0.002 > > ; Output control > > nstxout = 1000 > > nstvout = 1000 > > nstenergy = 1000 > > nstlog = 1000 > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Setting total simulation time
Try smaller numbers and periods for a test run, and see the machinery work. gmxcheck on the output files is your friend! Mark On Mon, Jun 3, 2013 at 4:40 PM, Parker de Waal wrote: > Hi GMX-users, > > If I wanted to run a 1 ns simulation take snapshots every 1 ps would these > be the correct input parameters? > > Thanks! > > ; Run parameters > integrator = md > nsteps = 50 > dt = 0.002 > ; Output control > nstxout = 1000 > nstvout = 1000 > nstenergy = 1000 > nstlog = 1000 > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Setting total simulation time
Hi GMX-users, If I wanted to run a 1 ns simulation take snapshots every 1 ps would these be the correct input parameters? Thanks! ; Run parameters integrator = md nsteps = 50 dt = 0.002 ; Output control nstxout = 1000 nstvout = 1000 nstenergy = 1000 nstlog = 1000 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
