[gmx-users] factor of 1.25 in lipid and GROMOS87 parameter

[Rakesh Gupta]

Dear gmx users

I am using berger force field for the simulation of lipid bilayers which is
combination of gromos87 and OPLS. Could any one explain how the cross non
bonded parameters (c6 and c12) were calculated in lipid.itp(
http://wcm.ucalgary.ca/tieleman/downloads).

I took LP2 parameter from the original paper of Berger et al. (sigma= 0.396
nm & epsilon = 0.380 KJ/mole) and calculated cross non bonded parameters
with the gromos87 atoms (taken from ffgmxnb.itp) using two different
combination rules.

Parameters in lipid.itp file:

Atom1  Atom2                C6                     C12

LP2         O             0.004536057       5.11881E-06

LP2         OA          0.004536057       7.29511E-06

LP2         N             0.004707795       7.73289E-06

LP2         NL           0.004707795       7.73289E-06

LP2         C             0.004614105       1.09185E-05

LP2         CH1        0.01066219          5.03492E-05

LP2         CH2        0.0090975            0.000035333

LP2         CH3        0.008986321       3.03967E-05

LP2         CR51      0.007082114       2.31135E-05

LP2         CR61      0.007082114       2.31135E-05

LP2         CB           0.004614105       1.09185E-05

LP2         CA          0.003024038       4.19474E-06

LP2         CR5        0.007082114       2.31135E-05

LP2         CR6        0.007082114       2.31135E-05

LP2         SD           0.009801974       2.75613E-05

LP2         CD          0.00907407          2.77268E-05


 Rule 1.  LB  Rule

Atom1  Atom2
   C6                       C12              C6(lip)/C6(LB)  C12(lip)/C12(LB)

LP2         O             0.00412867          5.26432E-06
1.098672611       0.972359193

LP2         OA          0.003881794       6.63207E-06
1.168546644       1.099973399

LP2         N             0.004016561       6.98756E-06
1.172095988       1.106665199

LP2         NL           0.004016561       6.98756E-06
1.172095988       1.106665199

LP2         C             0.003779043       9.09204E-06
1.220971824       1.200885214

LP2         CH1        0.008586694       4.05379E-05
1.241710785       1.242027167

LP2         CH2        0.007302453       2.82608E-05
1.245814281       1.250249232

LP2         CH3        0.007224107       2.4386E-05
1.243935254       1.246480609

LP2         CR51      0.005698494       1.85768E-05        1.24280447
        1.24421536

LP2         CR61      0.005698494       1.85768E-05        1.24280447
        1.24421536

LP2         CB           0.003779043       9.09204E-06
1.220971824       1.200885214

LP2         CA          0.002648798       3.99519E-06
1.141664438       1.049946084

LP2         CR5        0.005698494       1.85768E-05        1.24280447
         1.24421536

LP2         CR6        0.005698494       1.85768E-05        1.24280447
         1.24421536

LP2         SD           0.007935071       2.24225E-05
1.235272319       1.229179591

LP2         CD          0.007317596       2.23842E-05
1.240034275       1.238674874


 Rule 2        Geometric mixing (GM) rule

Atom1  Atom2                 C6                    C12
C6(lip)/C6(GM)     C12(lip)/C12(GM)

LP2         O             0.003641035       4.09423E-06
1.245815129       1.250251168

LP2         OA          0.003641034       5.83491E-06
1.245815687       1.250252433

LP2         N             0.003778885       6.18506E-06
1.245815856       1.250252111

LP2         NL           0.003778885       6.18506E-06
1.245815856       1.250252111

LP2         C             0.003703683       8.73304E-06
1.245815186       1.250251659

LP2         CH1        0.008558403       4.02712E-05
1.245815403       1.250252172

LP2         CH2        0.007302446       2.82607E-05
1.245815394       1.250251484

LP2         CH3        0.007213204       2.43125E-05
1.245815422       1.250251594

LP2         CR51      0.005684721       1.84871E-05        1.24581552
        1.250251466

LP2         CR61      0.005684721       1.84871E-05        1.24581552
        1.250251466

LP2         CB           0.003703683       8.73304E-06
1.245815186       1.250251659

LP2         CA          0.002427357       3.35512E-06
1.245815329       1.250251403

LP2         CR5        0.005684721       1.84871E-05        1.24581552
         1.250251466

LP2         CR6        0.005684721       1.84871E-05        1.24581552
         1.250251466

LP2         SD           0.007867916       2.20446E-05
1.245815714       1.250252199

LP2         CD          0.007283638       2.2177E-05
1.245815582       1.250251765


When I used LB rule the cross non bonded parameters were not similar to
lipid.itp. While in case of GM rule the cross parameters(c6 and c12) were
less then a factor of 1.25 as compare to lipid.itp. Can any one explain why
this factor of 1.25 is arising.


-- 
--
Regards
RAKESH GUPTA