Hi, I'm trying to use umbrella pulling to do a targeted MD and I have the following pull code: pull = umbrella pull_geometry = distance pull_dim = N N Y pull_start = no pull_ngroups = 1 pull_group0 = REF pull_group1 = PULL pull_init1 = 5 pull_rate1 = -0.0005 ; nm/ps pull_k1 = 1000 ; kJ mol^-1 nm^-2
which gives the results: (position.xvg) Time Z(nm) dZ(nm) 0.0000 12.1868 5.04599 0.0100 12.1868 5.04576 0.0200 12.1869 5.04552 0.0300 12.1869 5.0453 0.0400 12.1869 5.04508 0.0500 12.1869 5.04486 0.0600 12.187 5.04465 0.0700 12.1869 5.04447 0.0800 12.1869 5.04423 0.0900 12.1869 5.044 0.1000 12.1869 5.04376 0.1100 12.1869 5.04351 0.1200 12.1868 5.04333 0.1300 12.1868 5.04304 0.1400 12.1868 5.04274 0.1500 12.1868 5.04242 0.1600 12.1868 5.04208 0.1700 12.1866 5.04183 0.1800 12.1866 5.04145 0.1900 12.1866 5.04105 0.2000 12.1866 5.04063 0.2100 12.1866 5.0402 0.2200 12.1864 5.03985 0.2300 12.1864 5.03939 0.2400 12.1864 5.03891 0.2500 12.1864 5.03843 0.2600 12.1864 5.03795 0.2700 12.186 5.03762 0.2800 12.186 5.03715 0.2900 12.186 5.03669 0.3000 12.186 5.03626 0.3100 12.186 5.03586 (force.xvg): Time Force 0.0000 -45.9932 0.0100 -45.7626 0.0200 -45.5344 0.0300 -45.3134 0.0400 -45.0967 0.0500 -44.8854 0.0600 -44.6768 0.0700 -44.5008 0.0800 -44.2741 0.0900 -44.045 0.1000 -43.8105 0.1100 -43.5675 0.1200 -43.3877 0.1300 -43.107 0.1400 -42.8104 0.1500 -42.4967 0.1600 -42.1648 0.1700 -41.915 0.1800 -41.538 0.1900 -41.1422 0.2000 -40.7282 0.2100 -40.3026 0.2200 -39.9637 0.2300 -39.5006 0.2400 -39.0298 0.2500 -38.5553 0.2600 -38.0832 0.2700 -37.7541 0.2800 -37.2857 0.2900 -36.8358 0.3000 -36.4099 0.3100 -36.0136 Can anyone tell me If the equilibrium position of the applied harmonic potential is the same as it is in pull_geometry = position (which is P_eq = P_REF + pull_init1 + time*pull_rate1*pull_vec1, where P_REF is the position of the reference group in my case ) and if the change of the equilibrium position of the applied harmonic potential is evaluated every single step (in my case every 0.01 ps )or every ps? What's more, is the force in the output evaluated according to the following equation so that only the z-component of the force ( which is a vector ) is reported in force.xvg? f = pull_k1*( P_eq - P_PULL ) = pull_k1*( P_REF - P_PULL + pull_init1 + time*pull_rate1*pull_vec1) = pull_k1*( pull_init1 - dZ - time*pull_rate1*pull_vec1) , where P_PULL is the position of the pulled group and dZ is the values in the 3rd column of position.xvg output. Finally, is umbrella pulling a good choice to do targeted MD ( the 'fast-growth' method proposed by C.Jarzynski )? Is there better way to do that in Gromacs? Thanks, Dejun Lin-- 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
