Merge pull request #856 from akohlmey/fix_srp_bugfix

# Solvated 5-mer peptide

# Demonstrating temper_npt

units		real

atom_style	full

pair_style	lj/charmm/coul/long 8.0 10.0 10.0

bond_style      harmonic

angle_style     charmm

dihedral_style  charmm

improper_style  harmonic

kspace_style	pppm 0.0001

read_data	data.peptide

neighbor	2.0 bin

neigh_modify	delay 5

timestep	2.0

thermo_style	custom step temp epair emol etotal press density

thermo		50

variable	temper_T world 275 280 285 290 295 300 305 310

variable 	rep world 0 1 2 3 4 5 6 7 

fix		myfix all npt temp ${temper_T} ${temper_T} 100.0 iso 1 1 1000

run		500

temper_npt	2000 100 ${temper_T} myfix 0 58728 1 

fix		2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31

group		peptide type <= 12

  rmax = sqrt(rsqmax);

  double cutneighmax_srp = neighbor->cutneighmax + 0.51*rmax;

  // find smallest cutghost

  double cutghostmin = comm->cutghost[0];

  if (cutghostmin > comm->cutghost[1])

    cutghostmin = comm->cutghost[1];

  if (cutghostmin > comm->cutghost[2])

    cutghostmin = comm->cutghost[2];

  double length0,length1,length2;

  if (domain->triclinic) {

    double *h_inv = domain->h_inv;

    length0 = sqrt(h_inv[0]*h_inv[0] + h_inv[5]*h_inv[5] + h_inv[4]*h_inv[4]);

    length1 = sqrt(h_inv[1]*h_inv[1] + h_inv[3]*h_inv[3]);

    length2 = h_inv[2];

  } else length0 = length1 = length2 = 1.0;

  // find smallest cutghost.

  // comm->cutghost is stored in fractional coordinates for triclinic

  double cutghostmin = comm->cutghost[0]/length0;

  if (cutghostmin > comm->cutghost[1]/length1)

    cutghostmin = comm->cutghost[1]/length1;

  if (cutghostmin > comm->cutghost[2]/length2)

    cutghostmin = comm->cutghost[2]/length2;

  // stop if cutghost is insufficient

  if (cutneighmax_srp > cutghostmin){