[gmx-users] How to set up the cut-off radius

[Yanmei Song]

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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