What you've done looks reasonable. Depending on how unstable the RMSD is, you may just have to simulate longer.
Always remember to use a pertinent subject line when sending messages. That way more people are likely to respond if they see something of interest! -Justin Quoting minnale <[EMAIL PROTECTED]>: > > Hi all, > I ran protein simulation in water for 9ns and plotted RMSD but it didnt > stabilize, iam doubting on steps what I have done > I am mentioning the steps > > 1.EM in vaccum > 2.PR in vaccum in NVT > 3.EM in water > 4.PR in water in NVT > 5.Production run for 250 ps in NPT remain 9ns run in MVT condition > 6. Intersected the protein residues from whole protein > so I have used > make_ndx -f protein.gro -n r_20-50.ndx > selected 1 & r 20-50 means in whole protein select from res 20-50 > 7.g_rms -f 9ns_prot.xtc -n r_20-50.ndx -pbc -s min_wat.gro -o rms_9ns.xvg > Here I have selected "protein&r_20-50" for group least square fit and > then selected " group 3(c-alpha)" for RMSD calculation > > In above mentioned steps did I do any where wrong > I am pasting my md.mdp file > title = dpt_prod > constraints = hbonds > integrator = md > dt = 0.002 ; ps ! > nsteps = 500000 ; total 250 ps. > nstcomm = 1 > nstxout = 100 > nstlog = 100 > nstenergy = 100 > nstlist = 10 > ns_type = grid > coulombtype = PME > rlist = 0.9 > rcoulomb = 0.9 > rvdw = 1.4 > pbc = xyz > comm_grps = Protein > ; Berendsen temperature coupling is on in two groups > Tcoupl = Berendsen > tc-grps = Protein SoL_CL- > tau_t = 0.1 0.1 > ref_t = 300 300 > ; isotropic pressure coupling is off > Pcoupl = no > pcoupltype = isotropic > tau_p = 0.5 > compressibility = 4.5e-5 > ref_p = 1.0 > ; Energy monitoring > energygrps = Protein SOL_CL- > ; Generate velocites is off at 300 K. > gen_vel = no > gen_temp = 300 > gen_seed = 173529 > ~ > > Waiting for invaluable suggestion > Thanks in advance > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
