Dear Andrish Reddy,
Dont know if it works but I have for small molecules just put all the parmeters within the .top file right below the defaults, instead of user defined tables, and removed the "forcefieldX/SPC.itp" or equivalent section so it doesn't loop, but dont know if it works in your case. Just a quick suggestion to try, as I parse e-mails. Smone else probably has better answeres though...
Stephan
Gesendet: Mittwoch, 22. Mai 2013 um 16:09 Uhr
Von: "Andrish Reddy" <are...@csir.co.za>
An: gmx-users@gromacs.org
Betreff: [gmx-users] C6 & C12 parameters for non-bonded interactions using tables
Von: "Andrish Reddy" <are...@csir.co.za>
An: gmx-users@gromacs.org
Betreff: [gmx-users] C6 & C12 parameters for non-bonded interactions using tables
Greetings,
I am trying to use tabulated potentials for the VdW interactions between
TIP5P water molecules.
I have tested my topology file to make sure that it gives reasonable results
with the standard table6-12.xvg in the /top folder and C6=4*eps*sig^6 ,
C12=4*eps*sig^12. I am able to match the energies with an identical run not
using look-up tables. The problem comes when I want to include the C6 & C12
parameters within the table. This is needed for dealing with more complex
multi-parameter potential functions.
I tried testing this with the standard Lennard-Jones potential. Setting
g(r)=-(4*eps*sig^6)/r^6 and h(r)=(4*eps*sig^12)/r^12. I then construct my
table according to [r,f(r),-f'(r),g(r),-g'(r),h(r),-h'(r)]
I set vdw-type = user in my mdp file and modified my topology so that:
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 1 yes 0.5 0.8333
[ atomtypes ]
; name at.num mass charge ptype C6 C12
OW_tip5p 8 16.00 0.0000 A 1.00000e+00 1.00000e+00
Since C6 & C12 = 1, this run should be identical to using the table6-12.xvg
and C6=4*eps*sig^6 , C12=4*eps*sig^12
The run proceeds fine with no warnings or errors, but the LJ and Potential
energies are an order of magnitude higher than when using the standard
table. I don't understand why I am not able to reproduce the results by this
method?
Thanks,
Andrish
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I am trying to use tabulated potentials for the VdW interactions between
TIP5P water molecules.
I have tested my topology file to make sure that it gives reasonable results
with the standard table6-12.xvg in the /top folder and C6=4*eps*sig^6 ,
C12=4*eps*sig^12. I am able to match the energies with an identical run not
using look-up tables. The problem comes when I want to include the C6 & C12
parameters within the table. This is needed for dealing with more complex
multi-parameter potential functions.
I tried testing this with the standard Lennard-Jones potential. Setting
g(r)=-(4*eps*sig^6)/r^6 and h(r)=(4*eps*sig^12)/r^12. I then construct my
table according to [r,f(r),-f'(r),g(r),-g'(r),h(r),-h'(r)]
I set vdw-type = user in my mdp file and modified my topology so that:
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 1 yes 0.5 0.8333
[ atomtypes ]
; name at.num mass charge ptype C6 C12
OW_tip5p 8 16.00 0.0000 A 1.00000e+00 1.00000e+00
Since C6 & C12 = 1, this run should be identical to using the table6-12.xvg
and C6=4*eps*sig^6 , C12=4*eps*sig^12
The run proceeds fine with no warnings or errors, but the LJ and Potential
energies are an order of magnitude higher than when using the standard
table. I don't understand why I am not able to reproduce the results by this
method?
Thanks,
Andrish
--
View this message in context: http://gromacs.5086.x6.nabble.com/C6-C12-parameters-for-non-bonded-interactions-using-tables-tp5008449.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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