<div><span dir="ltr">Hi all.</span></div><div><span dir="ltr">I'm trying to learn how to use cp2k by myself.</span></div><div><span dir="ltr">I have managed to do a metadynamic but I am not able to obtain the fes.dat, in the first message you wrote that you compiled fes.dat.</span></div><div>But i don't find how i can compile it, can someone help me?.</div><div><span dir="ltr">sorry if i write meaningless things, but i'm lost.</span></div><div>thanks.</div><div><br /></div><div>Nacho<br /><br /></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">El sábado, 1 de diciembre de 2007 a las 0:05:13 UTC+1, luca escribió:<br/></div><blockquote class="gmail_quote" style="margin: 0 0 0 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Hi all,<br>I am trying to get familiar with cp2k metadynamics calculation.<br>How can I plot the free energy profile as function of collective variable ?<br>What type of information are writed in standar output file like COLVAR,HILL,FREE_ENERGY_INFO etc... <br>Can I use these informations for plot free energy profile?<p>I compiled fep.sopt (In /cp2k/makefile directory I type: make fep.sopt)<br>and I have a standard input for MM molecular dynamics.<br>This is my input file. <br>(There are some imprecisions but it is only an example....)<p>&FORCE_EVAL <br> METHOD FIST<br> &MM <br> &FORCEFIELD <br> PARM_FILE_NAME ./par_amber2charmm.inp<br> PARMTYPE CHM <br> EI_SCALE14 0.8333<br> VDW_SCALE14 0.5<br> &SPLINE<br> UNIQUE_SPLINE T<br> RCUT_NB 10.0<br> &END SPLINE<br> &END FORCEFIELD <br> <br> &POISSON <br> &EWALD <br> EWALD_TYPE NONE<br> ALPHA 0.44<br> GMAX 64 <br> O_SPLINE 6 <br> &END EWALD <br> PERIODIC XYZ <br> &END POISSON<p> &END MM<br> <br> &SUBSYS<br> <br> &CELL <br> ABC 64.000 64.0 57.000<br> UNIT ANGSTROM <br> PERIODIC XYZ<br> &END CELL <p> &TOPOLOGY <br> COORD_FILE_NAME 3HS_H_2.coor<br> COORDINATE pdb<br> CONN_FILE_NAME 3HS.psf<br> CONNECTIVITY UPSF<br> &END TOPOLOGY <br> <br> &COLVAR <br> &DISTANCE<br> ATOMS 5200 1300 <br> &END DISTANCE<br> &END COLVAR<p> &COLVAR <br> &DISTANCE<br> ATOMS 5201 250<br> &END DISTANCE<br> &END COLVAR<p> &COLVAR <br> &DISTANCE<br> ATOMS 5201 1305<br> &END DISTANCE<br> &END COLVAR<br> &END SUBSYS <p> &END FORCE_EVAL <p>&GLOBAL <br> PRINT_LEVEL LOW<br> PROJECT HS_Bind<br> RUN_TYPE MD<br> SAVE_MEM F<br> TRACE F<br>&END GLOBAL <br> <br>&MOTION <p> &MD <br> ENSEMBLE NVT <br> STEPS 500000 <br> TIMESTEP 0.80 <br> TEMPERATURE 310.0<p> &THERMOSTAT<br> TYPE NOSE<br> REGION GLOBAL<br> &NOSE<br> &END NOSE<br> &END THERMOSTAT <p> &END MD<p> &FREE_ENERGY<br> &METADYN<br> NT_HILLS 100<br> WW 1.0E-3 <p> &METAVAR<br> COLVAR 1<br> &WALL<br> TYPE QUADRATIC<br> POSITION [angstrom] 4.0<br> &QUADRATIC<br> DIRECTION WALL_PLUS<br> K [kcalmol*angstrom^-2] 5.0<br> &END QUADRATIC <br> &END WALL<br> &END METAVAR<p> &METAVAR<br> COLVAR 2<br> SCALE 0.5<br> &WALL<br> TYPE QUADRATIC<br> POSITION [angstrom] 3.00<br> &QUADRATIC<br> DIRECTION WALL_PLUS<br> K [kcalmol*angstrom^-2] 5.0<br> &END QUADRATIC <br> &END WALL<br> &END METAVAR<p> &METAVAR<br> COLVAR 3<br> SCALE 0.5<br> &WALL<br> TYPE QUADRATIC<br> POSITION [angstrom] 4.00<br> &QUADRATIC<br> DIRECTION WALL_PLUS<br> K [kcalmol*angstrom^-2] 5.0 <br> &END QUADRATIC <br> &END WALL<br> &END METAVAR<p> &PRINT<br> &PROGRAM_RUN_INFO<br> EACH 50<br> FILENAME=3HS_info <br> &END PROGRAM_RUN_INFO <p> &COLVAR<br> EACH 50<br> FILENAME=3HS_colvar <br> &END COLVAR<p> &HILLS<br> EACH 50<br> FILENAME=3HS_hills<br> &END HILLS<br> <br> &END PRINT<br> <br> &END METADYN<p> &FREE_ENERGY_INFO<br> EACH 50<br> FILENAME =3HS_free<br> &END FREE_ENERGY_INFO<p> &END FREE_ENERGY<br> <br> &PRINT <br> &RESTART OFF <br> &END<br> &RESTART_HISTORY OFF <br> &END<p> &TRAJECTORY<br> <br> EACH 50<br> FORMAT DCD <br> &END<p> &VELOCITIES OFF <br> &END<br> &END PRINT <br>&END MOTION <br></p></p></p></p></p></p></p></p></p></p></p></p></p></p></p></p></p></p></p></p></p></p></blockquote></div>
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