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

[Justin Lemkul]

On 3/25/15 2:55 PM, Rakesh Gupta wrote:
> 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.
>
>

The pair-specific parameters in [nonbond_params] specifically override values 
generated by the combination rules.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================