hi<div><br></div><div>It seems that your couple-moltype is missing, that is, no molecules will be turned off interaction.</div><div><br></div><div><br></div><div>dawei<br><br><div class="gmail_quote">On Thu, Feb 17, 2011 at 8:26 AM, Moeed <span dir="ltr"><<a href="mailto:lecielll@googlemail.com">lecielll@googlemail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Hello Justin<br><br>Thanks for your attention. Just to remind you: I am getting blank dgdl and I found this in log file:<br clear="all">
<br>
> There are 0 atoms and 0 charges for free energy perturbation<br><br><br>====================================<br>EM<br>
><br>
> grompp -f em-l0.mdp -c *.gro -p PE60-0c-itp.top -o em-l0.tpr >&<br>
> output.grompp_em<br>
><br>
> mdrun -s em-l0.tpr -o em-l0.trr -c em-l0.gro -g  em-l0.log -e em-l0.edr<br>
> -v >& output.mdrun_em<br>
><br>
> MD<br>
><br>
> grompp -f md-l0.mdp -c em-l0.gro -p PE60-0c-itp.top -o md-l0.tpr -n<br>
> PE-HEX.ndx>& output.grompp_md<br>
><br>
> mdrun -s md-l0.tpr -o md-l0.trr -c md-l0.gro -g md-l0.log -e md-l0.edr<br>
> -x md-l0.xtc -dgdl md-l0.dgdl -v >& output.mdrun_md<br>================================<br>with mdp :<br><br><br>pbc          = xyz               <br>energygrps       = PE HEX<br>       <br>;      Run control<br>
integrator         = md            <br>dt                 = 0.002            <br>nsteps             = 500000 ;5000        <br>nstcomm            = 100            <br><br>;      Output control<br>nstenergy          = 100             <br>
nstxout            = 100             <br>nstvout            = 0<br>nstfout            = 0<br>nstlog             = 1000            <br>nstxtcout       = 1000            <br><br>;      Neighbor searching<br>
nstlist            = 10            <br>ns_type            = grid            <br><br>;      Electrostatics/VdW <br>;;;;coulombtype        = PME                   <br>vdw-type          = Shift       <br>
rcoulomb-switch    = 0              <br>rvdw-switch        = 0.9 ;0            <br><br>;      Cut-offs<br>rlist              = 1.1            <br>rcoulomb           = 1.1 ;1.0         <br>rvdw               = 1.0            <br>
<br>;      Temperature coupling   <br>Tcoupl             = v-rescale               <br>tc-grps            = System        <br>tau_t              = 0.1    ;0.1          <br>ref_t              = 400    ;300          <br>
<br><br>;      Velocity generation          <br>gen_vel            = yes            <br>gen_temp           = 300.0            <br>gen_seed           = 173529            <br><br>;      Bonds<br>constraints          = all-bonds           <br>
constraint-algorithm = lincs<br><br>;       Free energy control stuff<br>free_energy         =  yes<br>init_lambda         =  0 <br>delta_lambda        =  0<br>sc_alpha            =  0.5<br>sc-power            =  1<br>
sc_sigma            =  0.3<br>couple-lambda0      =  vdw<br>couple-lambda1      =  none<br>couple-intramol     =  no<br><br>***************************************<br>Thank you in advance.<br><font color="#888888">Moeed<br>
</font><br>--<br>
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