<HTML><HEAD><META content="text/html; charset=x-user-defined" http-equiv="Content-Type"><style type="text/css"><!--.MailHeader { font-family: "Arial"; font-size: 8pt; color: #000000; font-style: normal; font-weight: normal; text-decoration: none; }//--></style></HEAD><BODY><br ><font face="Arial" size="2"><TABLE STYLE="PADDING-LEFT: 5px; BORDER-BOTTOM-COLOR: blue; BORDER-LEFT: blue 1px solid; BORDER-TOP-COLOR: blue; BORDER-RIGHT-COLOR: blue"><tbody><TR><TD><br ><meta http-equiv="Content-Type" content="text/html; charset=x-user-defined" ><p>Dear Justin,<br ><br >Even with the new force field I am getting the same result. <br >The methanol. gro file , em.mdp, pr,mdp and md.mdp files looks like these<br ><br ><strong>Methanol, 1 bar, 300K, equilibrated using PME, BdG 21-09-2001<br >648<br >1MeOH Me1 1 1.970 1.460 1.209 -0.8587 -0.1344 -0.0643<br >1MeOH O2 2 1.978 1.415 1.082 0.0623 -0.1787 0.0036<br >1MeOH H3 3 1.905 1.460 1.030 -0.5020 -0.9564 0.0997<br >2MeOH Me1 4 2.013 0.181 0.123 0.0317 0.4268 -0.0034<br >2MeOH O2 5 1.980 0.097 0.224 -0.8424 -0.0021 -0.6308<br >2MeOH H3 6 2.060 0.100 0.284 -0.7967 -0.7548 -0.6455<br >3MeOH Me1 7 2.008 0.409 0.498 -0.6920 0.4374 0.2455<br >3MeOH O2 8 2.109 0.460 0.422 -0.6105 0.1049 0.1322<br >3MeOH H3 9 2.170 0.506 0.486 -0.6959 -1.9809 1.8452<br >4MeOH Me1 10 1.856 1.779 1.151 -0.2574 0.2271 -0.0352<br >4MeOH O2 11 1.951 1.877 1.153 0.0214 -0.0482 0.2841<br ></strong><br ><br ><strong>EM.mdp....<br ></strong><br >; VARIOUS PREPROCESSING OPTIONS = <br >title = mellitin<br >cpp = /lib/cpp<br >define = -DFLEXIBLE</p><p>; RUN CONTROL PARAMETERS = <br >integrator = steep<br >; start time and timestep in ps = <br >tinit = 0<br >dt = 0.001<br >nsteps = 4000<br >nstlist =10<br >ns_type =grid<br >rlist =0.5<br >rcoulomb =1.4<br >vdwtype =cutoff<br >rvdw =0.8</p><p>; ENERGY MINIMIZATION OPTIONS = <br >emtol = 0.00001<br >emstep = 0.1<br >nstcgsteep = 1000</p><p><strong>PR.mdp.....</strong><br ><br >warnings = 10<br >cpp = /lib/cpp<br >define = -DPOSRES<br >constraints = all-bonds<br >integrator = md<br >dt = 0.002 ; ps !<br >nsteps = 1000 ; total 1.0 ps.<br >nstcomm = 1<br >nstxout = 10<br >nstvout = 1000<br >nstfout = 0<br >nstlog = 10<br >nstenergy = 10<br >nstlist = 10<br >ns_type = grid<br >rlist = 0.5<br >rcoulomb = 1.4<br >rvdw = 0.8<br >epsilon_r = 66<br >; Berendsen temperature coupling is on in two groups<br >Tcoupl = nose-hoover<br >tau_t = 0.1 0.1<br >tc-grps = Protein other<br >ref_t = 300 300 <br >; Pressure coupling is not on<br >Pcoupl = no<br >tau_p = 0.5<br >compressibility = 4.5e-5<br >ref_p = 1.0<br >; Generate velocites is on at 300 K.<br >gen_vel = yes<br >gen_temp = 300.0<br >gen_seed = 173529<br ><br ><strong>MD.mdp...<br ></strong><br >cpp = /lib/cpp<br >constraints = all-bonds<br >integrator = md<br >tinit = 100<br >dt = 0.002 ; ps !leapfrog algorithm 2fs timestep<br >nsteps = 1000000 ; total 2 ns.<br >nstcomm = 1<br >nstxout = 10000<br >nstvout = 5000<br >nstfout = 0<br >nstlist = 10<br >ns_type = grid<br >rlist = 0.5<br >rcoulomb = 1.4<br >rvdw = 0.8<br >epsilon_r = 66.0<br >; Berendsen temperature coupling is on in two groups<br >Tcoupl = Berendsen<br >tau_t = 0.1 0.02<br >tc-grps = protein other<br >ref_t = 300 300<br >solvent_optimization = sol<br >; Energy monitoring<br >energygrps = Protein other<br >; Pressure coupling is not on<br >Pcoupl = Berendsen<br >tau_p = 2.0<br >compressibility = 4.5e-5<br >ref_p = 1.0<br >; Generate velocites is on at 300 K.<br >gen_vel = yes<br >gen_temp = 300.0<br >gen_seed = 173529<br ><br >------------------------------------------------------------------------------------<br ><br >I have mailed the itp for methanol that I am using in my previous mail. Kindly give me advice as to why I am getting similar results for water and methanol.<br ><br >Thanks..<br ><br >sharada<br ><br ></p></TD></TR></tbody></TABLE></font></BODY></HTML>