<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>

<p></p>

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