Dear All:<br><br><span style="color: rgb(204, 0, 0);">I am working on a large polymer molecule system. The single molecules has a dimension of 5nm. My question is how can I set up the cut-off in my md.mdp. I tried the cut-off of </span><span style="color: rgb(204, 0, 0);">1.2 </span><span style="color: rgb(204, 0, 0);">and got the following two notes:</span><br>
<br><br>NOTE 1 [file md.mdp, line unknown]:<br> The Berendsen thermostat does not generate the correct kinetic energy<br> distribution. You might want to consider using the V-rescale thermostat.<br><br>processing topology...<br>
Opening library file /packages/gromacs-4.0.4/share/gromacs/top/ffoplsaa.itp<br>Opening library file /packages/gromacs-4.0.4/share/gromacs/top/ffoplsaanb.itp<br>Opening library file /packages/gromacs-4.0.4/share/gromacs/top/ffoplsaabon.itp<br>
Generated 332520 of the 332520 non-bonded parameter combinations<br>Generating 1-4 interactions: fudge = 0.5<br>Generated 332520 of the 332520 1-4 parameter combinations<br>Excluding 3 bonded neighbours molecule type 'PDM'<br>
turning all bonds into constraints...<br>processing coordinates...<br>double-checking input for internal consistency...<br>Velocities were taken from a Maxwell distribution at 300 K<br>renumbering atomtypes...<br>converting bonded parameters...<br>
initialising group options...<br>processing index file...<br>Analysing residue names:<br>Opening library file /packages/gromacs-4.0.4/share/gromacs/top/aminoacids.dat<br>There are: 6 OTHER residues<br>There are: 0 PROTEIN residues<br>
There are: 0 DNA residues<br>Analysing Other...<br>Making dummy/rest group for Acceleration containing 1950 elements<br>Making dummy/rest group for Freeze containing 1950 elements<br>Making dummy/rest group for VCM containing 1950 elements<br>
Number of degrees of freedom in T-Coupling group PDM is 3903.00<br>Making dummy/rest group for User1 containing 1950 elements<br>Making dummy/rest group for User2 containing 1950 elements<br>Making dummy/rest group for XTC containing 1950 elements<br>
Making dummy/rest group for Or. Res. Fit containing 1950 elements<br>Making dummy/rest group for QMMM containing 1950 elements<br>T-Coupling has 1 element(s): PDM<br>Energy Mon. has 1 element(s): PDM<br>Acceleration has 1 element(s): rest<br>
Freeze has 1 element(s): rest<br>User1 has 1 element(s): rest<br>User2 has 1 element(s): rest<br>VCM has 1 element(s): rest<br>XTC has 1 element(s): rest<br>Or. Res. Fit has 1 element(s): rest<br>
QMMM has 1 element(s): rest<br>Checking consistency between energy and charge groups...<br>Calculating fourier grid dimensions for X Y Z<br>Using a fourier grid of 56x63x65, spacing 0.118 0.116 0.119<br>Estimate for the relative computational load of the PME mesh part: 0.90<br>
<br>NOTE 2 [file aminoacids.dat, line 1]:<br> The optimal PME mesh load for parallel simulations is below 0.5<br> and for highly parallel simulations between 0.25 and 0.33,<br> for higher performance, increase the cut-off and the PME grid spacing<br>
<br>This run will generate roughly 3 Mb of data<br>writing run input file...<br><br><br clear="all"><b style="color: rgb(204, 0, 0);">#1: For the note 1, do I have to change to V-rescale thermostat. since I used Berendsen for my prior systems and i want to be consistent.<br>
#2: How large should the cut-off be? Do I have to set up the cut-off to be larger than the dimension of the single molecule?<br><br>
Thank you so much for your help in advance!</b>
<br>-- <br>Yanmei Song<br>Department of Chemical Engineering<br>ASU<br>