chris.neale at utoronto.ca
Thu Mar 27 22:41:01 CET 2008
Yes, the LO LO in atom type should be as Justin has mentioned.
Sudheer, please note that the original post that you quote below actually includes an example for LO LO
"LO LO 1 15.9994 0.000 A 2.96000e-01 8.87864e-01"
Also note that similar information is available in that post for pairtypes.
Also note that these parameters require a double pairs section. Please do a search for my posts on this method and read them carefully.
--- original message ---
> > 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
> > 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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