[gmx-users] OPLS-AA/L

[Justin A. Lemkul]

Quoting sudheer babu <sudheer.pbm07 at gmail.com>:

> Hi all ,
> I wanted to use OPLS-FF for POPC and Protein, I followed the procedure from
> archives and the link is
> *http://www.gromacs.org/pipermail/gmx-users/2006-September/023639.html*
> The steps I have done are
> 1. I added "atom types" from lipid.itp to ffoplsaanb.itp  here I got  no
> exponential values for "sigma" and positive exponential "epsilon" values
> when substituted in equations.
> (atom types)
>   ;name  name  charge  mass  charge  ptype  sigma        epsilon
>    LO    LO      1  15.9994   0.000   A     0.00011209814
> 2.90868792E+17;carbonyl O, OPLS

I think you have done your calculations wrong.  Check the formulas again
provided in Chris' post.  For example, if I calculate sigma and epsilon
according to his equation, I get:

sigma = 0.2959999302
epsilon = 0.8786943396

which seem much more reasonable, given the magnitudes of sigma and epsilon from
ffoplsaanb.itp.

-Justin

>
> 2. I added "pair types" from lipid.itp to ffoplsaanb.itp  same kind of
> values came for sigma and epsilon
>    [ pairtypes ]
>   ; i        j       func      sigma         epsilon
>    LO        LO         1    0.000112183829  3.61555415E+16
>
> 3. I added dihedral types from lipid.itp to ffoplsaabon.itp
>
>    LP2  LP2   3   9.2789   12.156  -13.120 -3.0597 26.240 -31.495
>
> 4. Changed OW  to opls_116 in ffoplsaa.itp file
> 5. Removed HW in ffoplsaa.itp file
>
> 6. I made toplogy like this
>
> #include "ffoplsaa.itp"
> #include "popc.itp"
> #include "spc.itp"
>
> (sytem name)
> (molecules)
> protein         1
> POPC        87
> Sol          2020
> all these .itp files included in protein.top file generated by pdb2gmx
> command in which took OPLS-FF
>
> 7.Later ran minimisation it went fine wihtout error
> 8. when I am trying to run equilibration, crashed  and showed segmentation
> fault
> The commands used are : grompp -f pr.mdp -c em.gro -p .top  -o  out.tpr
> mdrun -v -deffnm out
>
> Step 21, time 0.042 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 8904.457031 (between atoms 1124 and 1126) rms 126.620766
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>    1120   1121   96.2    0.1470   0.5591      0.1470
>    1121   1122   92.1    0.1530   5.3756      0.1530
>    1122   1123   90.5    0.1430  41.4380      0.1430
>    1123   1124   90.3    0.1610 235.0883      0.1610
>    1124   1125   91.1    0.1480 190.6947      0.1480
> segmentation fault.
>
> I have 3 doubts
> 1.The steps I followed is correct? any comments will be appreciated
> 2. No need to include nonbandparameters and parameters for lipid and gromos
> interactions from lipid.itp to ffoplsaa.itp ?
> 3.  LO    HW     1 0.00000e+00  0.00000e+00 in this line how we will remove
> only HW without changing LO ?
> Pls suggest me detail explanation
> All comments will be appreciated
> Thanks in advance.
>



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Justin A. Lemkul
Graduate Research Assistant
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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