Hi everyone,<div><br></div><div>I had been trying to work with forces of the atoms and stumbled upon something weird. </div><div><br></div><div>In my md.mdp file i ask to write forces with a certain frequency then the grompp shows a seemingly harmless note, the full md.mdp and extract of the grompp.out are as follows :-</div>
<div><br></div><div><div>title = Yo</div><div>cpp = /usr/bin/cpp</div><div>constraints = none</div><div>integrator = md</div><div>dt = 0.002<span class="Apple-tab-span" style="white-space:pre"> </span>; ps !</div>
<div>nsteps = 8500<span class="Apple-tab-span" style="white-space:pre"> </span>; total 17 ps.</div><div>nstcomm = 0</div><div>nstxout = 500</div><div>nstvout = 500</div>
<div><b>nstfout = 500</b></div><div>nstlog = 100</div><div>nstenergy = 10</div><div>nstlist = 10</div><div>ns_type = grid</div><div>rlist = 1.3</div>
<div>coulombtype<span class="Apple-tab-span" style="white-space:pre"> </span> = Reaction-Field-zero</div><div>rcoulomb = 1.0</div><div>epsilon_rf<span class="Apple-tab-span" style="white-space:pre"> </span> = 0</div>
<div>vdwtype<span class="Apple-tab-span" style="white-space:pre"> </span> = Shift</div><div>rvdw = 1.0</div><div>rvdw_switch<span class="Apple-tab-span" style="white-space:pre"> </span> = 0.9</div>
<div>Tcoupl = no</div><div>energygrps = DPPC SOL</div><div>Pcoupl = no</div><div>gen_vel = no</div><div>lincs_iter<span class="Apple-tab-span" style="white-space:pre"> </span> = 2</div>
<div><br></div><div><div>Ignoring obsolete mdp entry 'title'</div><div>Ignoring obsolete mdp entry 'cpp'</div><div>checking input for internal consistency...</div><div>Opening library file /home/hpc-23/vedadi/gromacs-4.0.5/tmp/share/gromacs/top/ffgmx.itp</div>
<div>Opening library file /home/hpc-23/vedadi/gromacs-4.0.5/tmp/share/gromacs/top/ffgmxnb.itp</div><div>Opening library file /home/hpc-23/vedadi/gromacs-4.0.5/tmp/share/gromacs/top/ffgmxbon.itp</div><div>Opening library file /home/hpc-23/vedadi/gromacs-4.0.5/tmp/share/gromacs/top/ff_dum.itp</div>
<div>Generated 1369 of the 2211 non-bonded parameter combinations</div><div>Opening library file /home/hpc-23/vedadi/gromacs-4.0.5/tmp/share/gromacs/top/spc.itp</div><div>Excluding 3 bonded neighbours molecule type 'DPPC'</div>
<div>Excluding 2 bonded neighbours molecule type 'SOL'</div><div>processing coordinates...</div><div>double-checking input for internal consistency...</div><div>renumbering atomtypes...</div><div>converting bonded parameters...</div>
<div>initialising group options...</div><div>processing index file...</div><div>Opening library file /home/hpc-23/vedadi/gromacs-4.0.5/tmp/share/gromacs/top/aminoacids.dat</div><div>Making dummy/rest group for T-Coupling containing 1933647 elements</div>
<div>Making dummy/rest group for Acceleration containing 1933647 elements</div><div>Making dummy/rest group for Freeze containing 1933647 elements</div><div>Making dummy/rest group for VCM containing 1933647 elements</div>
<div>Number of degrees of freedom in T-Coupling group rest is 3924894.00</div><div>Making dummy/rest group for User1 containing 1933647 elements</div><div>Making dummy/rest group for User2 containing 1933647 elements</div>
<div>Making dummy/rest group for XTC containing 1933647 elements</div><div>Making dummy/rest group for Or. Res. Fit containing 1933647 elements</div><div>Making dummy/rest group for QMMM containing 1933647 elements</div><div>
T-Coupling has 1 element(s): rest</div><div>Energy Mon. has 2 element(s): DPPC SOL</div><div>Acceleration has 1 element(s): rest</div><div>Freeze has 1 element(s): rest</div><div>User1 has 1 element(s): rest</div>
<div>User2 has 1 element(s): rest</div><div>VCM has 1 element(s): rest</div><div>XTC has 1 element(s): rest</div><div>Or. Res. Fit has 1 element(s): rest</div><div>QMMM has 1 element(s): rest</div>
<div>Checking consistency between energy and charge groups...</div><div><br></div><div><b>NOTE 1 [file nve.mdp, line unknown]:</b></div><div> This run will generate roughly 2493 Mb of data</div><div><br></div><div>writing run input file...</div>
<div><br></div><div>There was 1 note</div><div><br></div><div>gcq#197: "I Do It All the Time" (Magnapop)</div><div><br></div><div> :-) G R O M A C S (-:</div><div><br></div></div>
<div><br></div><div><br></div></div><div>Now when i change nstfout to zero (no printing of forces) the note doesnt show up anymore.</div><div><br></div><div>Also for the case with nstfout = 500 it seems that the forces are being read and written properly, I tried the g_traj tool to see the forces.</div>
<div><br></div><div>Could someone clarify?</div><div><br></div><div>Thank you,</div><div>Amit Choubey</div><div><br></div>