Dear gromacs users,<br><br> I am using gromacs 4.5.3, OPLSAA force field, and the cut off parameters<br>are as shown below:<br>---------------------------------------------------------------------------------------------<br>
;NEIGHBOURSEARCHING PARAMETERS<br>nstlist = 10 10 ; FREQUENCY WITH WHICH NEIGHBOURLIST IS UPDATED<br>ns_type = grid ; TYPE OF NEIGHBOUR SEARCH GRID OR SIMPLE<br>
pbc = xyz ; DIRECTION OF PERIODIC BOUNDARY CONDITIONS USAGE<br>rlist = 1.36 ; CUT-OFF DISTANCE FOR SHORT RANGE NEIGHBOUR LIST<br><br>;ELECTROSTATICS<br>
coulombtype = PME ; METHOD FOR CALCULATING COULOMBIC INTERCATION - PME<br>rcoulomb = 1.36 ; CUTOFF DISTANCE FOR ELECTROSTATIC INTERACTIONS<br>epsilon_r = 1 ; RELATIVE DIELECTRIC CONSTANT<br>
<br>;VAN DER WAALS<br>vdwtype = Switch ; METHOD FOR TREATING VANDERWAAL'S FORCES<br>rvdw_switch = 0.9 ; WHEN TO START SWITCHING LJ POTENTIAL<br>rvdw = 1.03 ; CUTOFF DISTANCE FOR LJ OR BUCKINGHAM INTERACTIONS<br>
<br>;EWALD<br>fourierspacing = 0.12 ; GRID SPACING FOR FFT GRID FOR PME<br>pme_order = 4 ; INTERPOLATION ORDER FOR PME<br>ewald_rtol = 1e-5 ; RELATIVE STRENGTH OF EWALD SHIFTED DIRECT POTENTIAL<br>
optimize_fft = yes ; SAVES A FEW PERCENT FOR LONG SIMULATIONS<br>-----------------------------------------------------------------------------------------------------<br><br>For EM (energy minimisation) I initially had used <br>
rlist = rcolomb = 1.2; rvdw = 1.1; rvdw_switch = 1.0<br>grompp gave the message:<br>##################<br>Largest charge group radii for Van der Waals: 0.160, 0.157 nm<br>Largest charge group radii for Coulomb: 0.168, 0.167 nm<br>
<br>NOTE 1 [file md.mdp]:<br> The sum of the two largest charge group radii (0.317) is larger than<br> rlist (1.20000) - rvdw (1.10000)<br>##################<br>So I changed the values to: rlist = rcolomb = 1.35; rvdw = 1.03; rvdw_switch = 1.0<br>
grompp message during em disappeared.<br><br>During PR (position refinement), Again the message appeared for grompp<br>##################<br>Largest charge group radii for Van der Waals: 0.168, 0.156 nm<br>
Largest charge group radii for Coulomb: 0.168, 0.164 nm<br><br>
NOTE 1 [file md.mdp]:<br>
The sum of the two largest charge group radii (0.324) is larger than<br>
rlist (1.35000) - rvdw (1.03000)<br>
##################<br>hence I changed the values to: rlist = rcolomb = 1.36; rvdw = 1.03; rvdw_switch = 1.0<br>grompp message during pr disappeared.<br><br>The same message repeated for MD <br>###################<br>Largest charge group radii for Van der Waals: 0.171, 0.159 nm<br>
Largest charge group radii for Coulomb: 0.171, 0.166 nm<br><br>NOTE 1 [file md.mdp]:<br> The sum of the two largest charge group radii (0.330248) is larger than<br> rlist (1.360000) - rvdw (1.030000)<br>###################<br>
<br>My questions are:<br>1. <span style="font-family: arial,helvetica,sans-serif;">Why does the charge group radii change in this way from em to pr to MD even though I </span><br style="font-family: arial,helvetica,sans-serif;">
<span style="font-family: arial,helvetica,sans-serif;"> am using same parameters</span><br style="font-family: arial,helvetica,sans-serif;"><span style="font-family: arial,helvetica,sans-serif;">2. What is the safest maximum value of rlist I can go up to? (is it 1.4nm according to "The Origin</span><br style="font-family: arial,helvetica,sans-serif;">
<span style="font-family: arial,helvetica,sans-serif;"> of Layer Structure</span> Artifacts in Simulations of Liquid Water"- JCTC, 2006, 2, 1-11 paper?)<span style="font-family: arial,helvetica,sans-serif;"> <br>3. What is the minimum safest rvdw distance i can take?<br>
4. According to the manual, when using switch they have suggested that ".. neighbor search<br> cut-off rlist should be 0.1 to 0.3nm larger than rvdw..." then Why in the above case it goes<br> more than 0.3nm?<br>
<br>Thanks in advance<br>MKS<br></span>