Hi all , <br>I wanted to use OPLS-FF for POPC and Protein, I followed the procedure from archives and the link is <br><u><a href="http://www.gromacs.org/pipermail/gmx-users/2006-September/023639.html">http://www.gromacs.org/pipermail/gmx-users/2006-September/023639.html</a></u><br>
The steps I have done are<br>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.<br>
(atom types) <br> ;name name charge mass charge ptype sigma epsilon<br> LO LO 1 15.9994 0.000 A 0.00011209814 2.90868792E+17 ;carbonyl O, OPLS<br> <br>2. I added "pair types" from lipid.itp to ffoplsaanb.itp same kind of values came for sigma and epsilon<br>
[ pairtypes ]<br> ; i j func sigma epsilon<br> LO LO 1 0.000112183829 3.61555415E+16<br> <br>3. I added dihedral types from lipid.itp to ffoplsaabon.itp <br><br> LP2 LP2 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495<br>
<br>4. Changed OW to opls_116 in ffoplsaa.itp file<br>5. Removed HW in ffoplsaa.itp file<br><br>6. I made toplogy like this <br><br>#include "ffoplsaa.itp"<br>#include "popc.itp"<br>#include "spc.itp"<br>
<br>(sytem name)<br>(molecules)<br>protein 1<br>POPC 87<br>Sol 2020<br>all these .itp files included in protein.top file generated by pdb2gmx command in which took OPLS-FF<br><br>7.Later ran minimisation it went fine wihtout error<br>
8. when I am trying to run equilibration, crashed and showed segmentation fault <br>The commands used are : grompp -f pr.mdp -c em.gro -p .top -o out.tpr<br>mdrun -v -deffnm out<br><br>Step 21, time 0.042 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>max 8904.457031 (between atoms 1124 and 1126) rms 126.620766<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br> 1120 1121 96.2 0.1470 0.5591 0.1470<br>
1121 1122 92.1 0.1530 5.3756 0.1530<br> 1122 1123 90.5 0.1430 41.4380 0.1430<br> 1123 1124 90.3 0.1610 235.0883 0.1610<br> 1124 1125 91.1 0.1480 190.6947 0.1480<br>
segmentation fault. <br><br>I have 3 doubts<br>1.The steps I followed is correct? any comments will be appreciated <br>2. No need to include nonbandparameters and parameters for lipid and gromos interactions from lipid.itp to ffoplsaa.itp ?<br>
3. LO HW 1 0.00000e+00 0.00000e+00 in this line how we will remove only HW without changing LO ?<br>Pls suggest me detail explanation <br>All comments will be appreciated<br>Thanks in advance.<br>