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