Thanks Justin, it seems to help, i have another general question that you might help me with:
should i define the distances for the umbrella sampling run in some file and then run it?(i saw something about *.ppa file but couldn't find any further instructions in the mannual..) will this file apply for the WHAM analysis after the run? thanks, Amir On Mon, Dec 28, 2009 at 6:14 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Amir Marcovitz wrote: > >> Hi, >> my system is constructed of 2 parallel plates in a box with solvent. each >> plate is made of 36 atoms which are positively charged on one of them (SRP) >> and negatively charged on the other plate (SRN). >> i want to perform a simulation with umbrella sampling between the 2 so i >> defined the pulling section parameters in the .mdp parameter file as >> following: >> ; COM PULLING ; Pull type: no, umbrella, constraint or >> constant_force >> pull = umbrella >> ; Pull geometry: distance, direction, cylinder or position >> pull_geometry = distance >> ; Select components for the pull vector. default: Y Y Y >> pull_dim = Y Y Y >> ; Cylinder radius for dynamic reaction force groups (nm) >> pull_r1 = 1 >> ; Switch from r1 to r0 in case of dynamic reaction force >> pull_r0 = 1.5 >> pull_constr_tol = 1e-06 >> pull_start = no >> pull_nstxout = 10 >> pull_nstfout = 1 >> ; Number of pull groups >> pull_ngroups = 2 >> ; Group name, weight (default all 1), vector, init, rate (nm/ps), >> kJ/(mol*nm^2) >> pull_group0 = SRP >> pull_weights0 = 1 >> pull_pbcatom0 = 0 >> pull_group1 = SRN >> pull_weights1 = 1 >> pull_pbcatom1 = 0 >> pull_vec1 = 0.0 1.0 0.0 >> pull_init1 = 1.5 >> pull_rate1 = 0 >> pull_k1 = 1 >> pull_kB1 = 0 >> when proccesing the file with grompp i get the following error: >> *Fatal error: >> Number of weights (1) for pull group 0 'SRP' does not match the number of >> atoms (36)* >> is someone recognizing my mistake? >> > > Please refer to the manual (manual.gromacs.org is quite handy), you will > find: > > "Optional relative weights which are multiplied with the masses of the > atoms to give the total weight for the COM. The number should be 0, meaning > all 1, or the number of atoms in the pull group." > > I also think your value for pull_ngroup is wrong. It appears you are > pulling SRN with respect to SRP, so you only have one pull group, not two. > > -Justin > > does someone has an experience with umbrella sampling in GROMACS? >> thanks' >> amir >> * >> * >> >> > -- > ======================================== > > 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 gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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