[gmx-users] (no subject)

[Daejoong Kim]

Hello all. This is what I posted a couple of weeks ago. Please reply to this.

I have two questions but the first one is very important to me.

1. About LJ parameters: sigma/epsilon vs. c6/c12
Instead of using "itp" files in GROMACS/share/top, I used the following two
"itp" files for non-bonded interactions. For me the two files are supposed
to produce the same results but they turn out to be very different. My
question is: for switching sigma/epsilon between c6/c12 can I just apply the
following relations without worrying about the unit issues? (which question
I thought is right but seemingly wrong now.)
c6 = 4 * epsilon * sigma^6
c12 = 4 * epsilon * sigma^12

(1) sigma/epsilon "itp" file 
[ defaults ]
; func_type   comb-rule   gen-pairs   fudgeLJ     fudgeQQ
          1           2          no       1.0         1.0

[ atomtypes ]
; name   mass  charge p_type      sigma     epsilon
    OW  0.000   0.000      A  0.3165648   0.6501673
     H  0.000   0.000      A  0           0
    NA  0.000   0.000      A  0.25754     0.061749
    CL  0.000   0.000      A  0.4447960   0.4457080
  SIO2  60.08   0.000      A  0.3         1.9123

[ nonbond_params ]
;   i     j f_type     sigma     epsilon
   NA    OW      1  0.285529    0.200368
   NA     H      1  0           0
   CL    OW      1  0.37524     0.53832
   CL     H      1  0           0
   CL    NA      1  0.33845     0.16590
 SIO2    OW      1  0.30828     1.1150
 SIO2     H      1  0.15000     0
 SIO2    NA      1  0.27877     0.34363
 SIO2    CL      1  0.37240     0.92322

[ pairtypes ]
;   i     j f_type     sigma     epsilon
   OW    OW      1  0.3113429   0.7184020
    H    OW      1  0           0
    H     H      1  0           0
   NA    OW      1  0.28316     0.21062
   NA     H      1  0           0
   NA    NA      1  0.25754     0.061749
   CL    OW      1  0.37213     0.56586
   CL     H      1  0           0
   CL    NA      1  0.33845     0.16590
   CL    CL      1  0.4447960   0.4457080
 SIO2  SIO2      1  0.3         1.9123
 SIO2    OW      1  0.30828     1.1150
 SIO2     H      1  0.15000     0
 SIO2    NA      1  0.27877     0.34363
 SIO2    CL      1  0.37240     0.92322

(2) c6/c12 "itp" file
[ defaults ]
; func_type   comb-rule   gen-pairs   fudgeLJ     fudgeQQ
          1           1          no       1.0         1.0

[ atomtypes ]
;name     mass      charge p_type           c6           c12
   OW     0.000      0.000     A  0.0026173456  2.634129e-06
    H     0.000      0.000     A           0           0
   NA     0.000      0.000     A  7.2063121e-05  2.1025e-08
   CL     0.000      0.000     A  0.01380625  0.0001069156
 SIO2     60.08      0.000     A  0.0055763   4.0651e-06

[ nonbond_params ]
;      i        j func           c6          c12
      NA       OW  1  0.00043429724  2.35335e-07
      NA        H  1           0           0
      CL       OW  1   0.0060113  1.678182e-05
      CL        H  1           0           0
      CL       NA  1  0.0009974575  1.4993e-06
    SIO2       OW  1  0.0038283     3.2861e-06
    SIO2        H  1           0           0
    SIO2       NA  1  6.4510e-04     3.0276e-07
    SIO2       CL  1  0.0098497     2.6271e-05

[ pairtypes ]
;      i        j f_type        c6           c12
      OW       OW  1  0.0026173456  2.383936e-06
       H       OW  1           0           0
       H        H  1           0           0
      NA       OW  1  0.00043429724  2.2388e-07
      NA        H  1           0           0
      NA       NA  1  7.2063121e-05  2.1025e-08
      CL       OW  1   0.0060113  1.596496e-05
      CL        H  1           0           0
      CL       NA  1  0.0009974575  1.4993e-06
      CL       CL  1  0.01380625  0.0001069156
    SIO2       OW  1  0.0038283   3.2861e-06
    SIO2        H  1           0           0
    SIO2       NA  1  6.45100e-04  3.0276e-07
    SIO2       CL  1  0.0098497   2.6271e-05
    SIO2     SIO2  1  0.0055763   4.0651e-06

Well, it is annoying. Besides choosing combination rule in [defaults]
section, do I need to do different things for two cases? Is it an issue of
units?

2. About charges and masses
Charges and masses can be finally changed in [atoms] section under
[moleculetype], right? I mean those values override the ones specified in
[atomtypes] or any other places? Am I right?

Thank you in advance.





Best regards,


Daejoong Kim
PhD candidate
Mechanical Engineering
Stanford University
phone:650-723-1028