[gmx-users] OPLS-AA/L

[sudheer babu]

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

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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