Dear gromacs users,<br><br>I am trying to calculate the PMF along the end-to-end distance for a short polymer (hexa-ethylene glycol), using the pull code in gromacs-4.0.4. I run grompp with: grompp_s -v -n OH_ends.ndx -f sd.mdp -c 0.425nm.pdb -p 6EG.top, where sd.mdp is:<br>
************************<br>title = <br>cpp = /usr/bin/cpp<br>integrator = sd<br>dt = 0.002 ; [ps]<br>nsteps = 1000000<br>nstcomm = 10 ; frequency for center of mass motion removal<br>
comm_mode = Linear ; Remove center of mass translation<br>comm_grps = system<br>nstxtcout = 10000 ; frequency to write coordinates to xtc trajectory<br>nstxout = 10000 ; frequency to write coordinates to output trajectory file<br>
nstvout = 100000<br>nstlog = 10000<br>nstenergy = 10000<br>energygrps = 6EG ; group(s) to write to energy file<br>pbc = no<br>nstlist = 0 ; neighbor list is only constructed once and never updated.<br>
ns_type = simple<br>rlist = 0 ; cut-off distance for the short-range neighbor list<br>rcoulomb = 0<br>rvdw = 0<br>tc-grps = 6EG<br>tau_t = 0.1 ; [ps]<br>
ref_t = 300 ; [K]<br>pull = umbrella<br>pull_geometry = distance<br>pull_init1 = 0.425 ; [nm]<br>pull_dim = Y Y Y<br>pull_ngroups = 1<br>pull_group0 = group 1<br>
pull_group1 = group 2<br>pull_k1 = 1000<br>************************<br>group 1 and group 2 are defined in OH_ends.ndx:<br>************************<br>[ group 1 ]<br> 1 2<br>[ group 2 ]<br> 20 21<br>
************************<br><br>and 6EG.top is:<br>************************<br>#include "ffgmx.itp"<br>#include "6EG.itp"<br>[ system ]<br>Hexa-ethylene glycol: Langevin dynamics<br>[ molecules ]<br>6EG 1<br>
************************<br><br>But, grompp fails with:<br>-------------------------------------------------------<br>Program grompp_s, VERSION 4.0.4<br>Source code file: readir.c, line: 1013<br><br>Fatal error:<br>Group 6EG not found in indexfile.<br>
Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp.<br>In that case use the '-n' option.<br>-------------------------------------------------------<br><br>But, I *am* using the -n option! If I include the group 6EG in the index file (I didn't think it was necessary since it is defined in the .top file), grompp chokes with:<br>
"Fatal error: Group group 1 not found in indexfile.", even though group 1 is defined in the .ndx file. <br><br>It works fine without the pulling options. I have searched the manual, wiki and mailing list archives for a solution, without success. This gromacs newbie is out of ideas -- any help is much appreciated.<br>
<br>thanks,<br>Vaithee<br>