But the best would be to grompp (NPT) windows (lets say every 10-20 frames) of your configuration and at the end of grompp you will see the actual distance the gromacs will consider.
Jan ________________________________ From: [email protected] [[email protected]] on behalf of Shilpi Chaurasia [[email protected]] Sent: Monday, April 23, 2012 3:59 PM To: [email protected] Subject: [gmx-users] g_dist explanation 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 thanks, Shilpi
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