Thanks for the explanation. I should have used apt values for nstxtcout to get what I want. Thanks again
Shilpi Il 23.04.12, "Justin A. Lemkul" <[email protected]> ha scritto: > > > On 4/23/12 10:59 AM, Shilpi Chaurasia wrote: > > Hi Gromacs users, > > > >I am using pull code to separate two units of a protein dimer. I have run the > >pulling simulation for 650 ps and got pullx.xvg and pullf.xvg files, where > >the > >data is printed at every 0.01 ps (according to pull_nstxout & pull_nstfout, > >both > >are 10 in this case) as given below > > > >0.0000 0.000322052 > >0.0100 0.173534 > >0.0200 0.297454 > >0.0300 0.416585 > >0.0400 0.519195 > >0.0500 0.597541 > >... > > > >Now, I want to calculate the distance between COM of two groups using g_dist > >and > >printing the output data in the same time steps as in .xvg files. I tried but > >the output data is printed at every 2ps steps as following: > > > > 0.0000000 8.0175037 -0.0010343 -0.0055513 8.0175018 > > 2.0000000 8.0188007 -0.0202498 -0.0114326 8.0187674 > > 4.0000000 8.0377693 -0.0229554 -0.0129814 8.0377254 > > 6.0000000 8.0435743 -0.0226321 -0.0043244 8.0435410 > > 8.0000000 8.0615864 -0.0312104 -0.0116682 8.0615177 > >... > > > >command used > >g_dist -f *.xtc -s *.tpr -n index.ndx -o dist.xvg -b 0 -dt 1 -e 650 > > > >I have also tried by using different values for 'dt' but it doesn't help. > >If someone could tell me how to control the time steps in g_dist output, in > >this > >case I want the output to be printed in the steps of 0.01 ps > > > > You can't print frames that aren't there. If you saved frames using > "nstxtcout = 1000" (assuming a time step of 2 fs), then you can't create > frames in between. You would need to do the run again, saving frames with > greater frequency. Note that doing so will likely make your trajectory file > quite a bit larger. > > -Justin > > -- > ======================================== > > 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/Support/Mailing_Lists/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/Support/Mailing_Lists > >
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