Hi, On Thursday, 15. May 2008 18:04, Justin A. Lemkul wrote: > Quoting minnale <[EMAIL PROTECTED]>: > > Thanks for your prompt reply Justin > > I am simulating 1ns each time, Due to this its happening? why i got this > > doubt because at each 1ns, graph is showing either lowside fluctuations > > or upside fluctuations. > > I don't understand what you mean.
have you mirrored your trajectory back to a normal box? Have you inspected it visually, does it always stay inside the box? If not use trjconv -pbc nojump -fit rot+trans greetings, Florian > > I doubt that you're causing any problems by simulating 1 ns at a time. The > best I can guess, you just need more time for your simulation to stabilize. > Without any knowledge of what it is, it's hard to say. Be aware that RMSD > can fluctuate quite widely until the structure is happy. > > -Justin > > > Thanks for any appreciation > > > > On Thu, 15 May 2008 Justin A.Lemkul wrote : > > >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/ > > > > > >======================================== > > ======================================== > > 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 -- ------------------------------------------------------------------------------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26573 Mailto: florian.haberl AT chemie.uni-erlangen.de ------------------------------------------------------------------------------- _______________________________________________ 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
