I tried using the nonbonded parameters as defined below in my
ffoplsaanb.itp file for methanol in water and this is the syntax I used:
[nonbond_params ]
;i j func c6 c12
opls_154 opls_111 1 0.00E+000 2.43E-006
opls_154 opls_112 1 0.00E+000 0.00E+000
opls_154 opls_112 1 0.00E+000 0.00E+000
opls_155 opls_111 1 0.00E+000 0.00E+000
opls_155 opls_112 1 0.00E+000 0.00E+000
opls_155 opls_112 1 0.00E+000 0.00E+000
opls_156 opls_111 1 0.00E+000 2.70E-007
opls_156 opls_112 1 0.00E+000 0.00E+000
opls_156 opls_112 1 0.00E+000 0.00E+000
opls_157 opls_111 1 0.00E+000 3.01E-006
opls_157 opls_112 1 0.00E+000 0.00E+000
When I tried to do mdrun, I got an error saying my system is
exploding. I tried doing the mdrun without nonbonded parameters and it
runs fine. So I am not sure if I am using the nonbond_params concept
correctly. i.e. I want C6 to be zero between my solute (methanol) and
solvent (water). This is the error:
Warning: 1-4 interaction between 2 and 6 at distance 3.786 which is
larger than the 1-4 table size 2.500 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
Suggestions?
Thanks.
-Nisha P
Quoting [email protected]:
Okay I am going to give it a try. I just wanted to make sure I was
calculating C6 and C12 correctly as well using sigma and epsilon
according to rule 3
C12 = Sigma^(6)*C6
C6 = 4*sigma^(6)*epsilon
Thanks
Quoting "Justin A. Lemkul" <[email protected]>:
[email protected] wrote:
Hello,
I have a concern regarding C6 attractive term in LJ potential. I
am using OPLS-AA force field, and I wish to turn off attractive
term C6 by setting the parameters to zero. One of the suggestion
was to add a [nonbond_params] in my ffoplsaanb.itp file and set
the C6 to zero between the non-bonded pair. In my system for
example, which consists of one methanol in water, I wish to set
C6 term to zero between my solute and solvent. Since OPLSAA is
all atom force field it treats each atom individually and has
sigma and epsilon for each atom, so I am not sure how I would
actually set my nonbond_params in my nb.itp file. I realize I
need to convert each sigma and epsilon to C6 and C12, so say for
example for methanol in water my [nonbond_params] would look
something like this?
[ nonbond_params ]
; i j func c6 c12
CT OW 1 0.00 calculated value for C12 here?
CT HW1 1 0.00
CT HW2 1 0.00
CT is the carbon in Methanol. OW, HW1 an HW2 correspond to atoms
in TIP3P water model
Is that correct? Would I have to do that for each atom in methanol?
Sounds about right to me.
-Justin
Any suggestions would be appreciated.
Thanks.
Nisha P
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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