Hello I am trying to perform some US calculations to obtain the potential of mean force of the insertion of a molecule inside a lipid bilayer. For that I follow the tutorial of Dr Justin Lemkul with some modifications and start the simulations with the following mdp
pull_group1_name = MEMB pull_group2_name = FEI pull_ngroups = 2 pull_ncoords = 1 pull-nstxout = 500 pull-nstfout = 500 pull_print_com1 = yes pull_print_ref-value = yes ;pull_print_components = yes pull_coord1_type = umbrella ; harmonic biasing force pull_coord1_geometry = distance ; simple direction decrease pull_coord1_groups = 1 2 pull_coord1_dim = N N Y pull_coord1_k = 1500 ;pull_coord1_rate = -0.01 pull_coord1_start = yes And indeed after 800 ps the molecule move to the bilayer center and the distance between the COMs of the molecule and the bilayer reported in the pullx file is close 0 nm. However when I do the second step of the tutorial with the perl script provide in the J. lemkul tutorial (perl_distance.pl) to select the US windows, the distance is greater than around 1 for the same config . see below the pullx = 800.0000 0.00105624 -4.02734 the COM-distance computed with perl script after the membrane was centered in the box with -pbc mol is 800 1.264 Why this difference, and to choose the good interval for the US sampling I use the following command trough the perl script distance_PMF$ gmx_mpi distance -s ./US_Files_step1/PHE_POPC_Memb_CHARMM_PMF_1500Kj_01rate_US_step1.tpr -f conf800.gro -n System.ndx -oall dist0.xvg -select 'com of group MEMB plus com of group FEI' Thank you in advance -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
