<P>
<BR>
If I use the command in this way with option -mir insted of -o<BR>
<BR>
g_rms -f 9ns.xtc -n r20-50.ndx -mir mirror.xvg -pbc -s min.gro <BR>
selected r_20-50 for least square fit group<BR>
selected c-alpha for RMSD calculation<BR>
<BR>
if I plot a graph by using mirror.xvg file there is no fluctuations after 4ns to 9ns I can say system is almost stabilised, but if i use -o option RMSD values are quite vary and system not yet stable even at 9ns<BR>
so shall i stop the simulation or continue the simulation some more time as Justin said. <BR>
sorry for the asking trivial questions.<BR>
Thanks for your appreciation <BR>
<BR>
n Thursday, 15. May 2008 18:04, Justin A. Lemkul wrote:<BR>
> Quoting minnale <minnale_gnos at rediffmail.com>:<BR>
> > Thanks for your prompt reply Justin<BR>
> > I am simulating 1ns each time, Due to this its happening? why i got this<BR>
> > doubt because at each 1ns, graph is showing either lowside fluctuations<BR>
> > or upside fluctuations.<BR>
><BR>
> I don't understand what you mean.<BR>
<BR>
<BR>
>have you mirrored your trajectory back to a normal box?<BR>
>Have you inspected it visually, does it always stay inside the box?<BR>
<BR>
>If not use trjconv -pbc nojump -fit rot+trans<BR>
<BR>
>greetings,<BR>
<BR>
Florian<BR>
<BR>
<BR>
<BR>
<BR>
><BR>
> I doubt that you're causing any problems by simulating 1 ns at a time. The<BR>
> best I can guess, you just need more time for your simulation to stabilize.<BR>
> Without any knowledge of what it is, it's hard to say. Be aware that RMSD<BR>
> can fluctuate quite widely until the structure is happy.<BR>
><BR>
> -Justin<BR>
><BR>
> > Thanks for any appreciation<BR>
> ><BR>
> > On Thu, 15 May 2008 Justin A.Lemkul wrote :<BR>
> > >What you've done looks reasonable. Depending on how unstable the RMSD<BR>
> > > is,<BR>
> ><BR>
> > you<BR>
> ><BR>
> > >may just have to simulate longer.<BR>
> > ><BR>
> > >Always remember to use a pertinent subject line when sending messages. <BR>
> > > That<BR>
> ><BR>
> > way<BR>
> ><BR>
> > >more people are likely to respond if they see something of interest!<BR>
> > ><BR>
> > >-Justin<BR>
> > ><BR>
> > >Quoting minnale <minnale_gnos at rediffmail.com>:<BR>
> > > > Hi all,<BR>
> > > > I ran protein simulation in water for 9ns and plotted RMSD but it<BR>
> > > > didnt stabilize, iam doubting on steps what I have done<BR>
> > > > I am mentioning the steps<BR>
> > > ><BR>
> > > > 1.EM in vaccum<BR>
> > > > 2.PR in vaccum in NVT<BR>
> > > > 3.EM in water<BR>
> > > > 4.PR in water in NVT<BR>
> > > > 5.Production run for 250 ps in NPT remain 9ns run in MVT condition<BR>
> > > > 6. Intersected the protein residues from whole protein<BR>
> > > > so I have used<BR>
> > > > make_ndx -f protein.gro -n r_20-50.ndx<BR>
> > > > selected 1 & r 20-50 means in whole protein select from res 20-50<BR>
> > > > 7.g_rms -f 9ns_prot.xtc -n r_20-50.ndx -pbc -s min_wat.gro -o<BR>
> > > > rms_9ns.xvg Here I have selected "protein&r_20-50" for group least<BR>
> > > > square fit and then selected " group 3(c-alpha)" for RMSD calculation<BR>
> > > ><BR>
> > > > In above mentioned steps did I do any where wrong<BR>
> > > > I am pasting my md.mdp file<BR>
> > > > title = dpt_prod<BR>
> > > > constraints = hbonds<BR>
> > > > integrator = md<BR>
> > > > dt = 0.002 ; ps !<BR>
> > > > nsteps = 500000 ; total 250 ps.<BR>
> > > > nstcomm = 1<BR>
> > > > nstxout = 100<BR>
> > > > nstlog = 100<BR>
> > > > nstenergy = 100<BR>
> > > > nstlist = 10<BR>
> > > > ns_type = grid<BR>
> > > > coulombtype = PME<BR>
> > > > rlist = 0.9<BR>
> > > > rcoulomb = 0.9<BR>
> > > > rvdw = 1.4<BR>
> > > > pbc = xyz<BR>
> > > > comm_grps = Protein<BR>
> > > > ; Berendsen temperature coupling is on in two groups<BR>
> > > > Tcoupl = Berendsen<BR>
> > > > tc-grps = Protein SoL_CL-<BR>
> > > > tau_t = 0.1 0.1<BR>
> > > > ref_t = 300 300<BR>
> > > > ; isotropic pressure coupling is off<BR>
> > > > Pcoupl = no<BR>
> > > > pcoupltype = isotropic<BR>
> > > > tau_p = 0.5<BR>
> > > > compressibility = 4.5e-5<BR>
> > > > ref_p = 1.0<BR>
> > > > ; Energy monitoring<BR>
> > > > energygrps = Protein SOL_CL-<BR>
> > > > ; Generate velocites is off at 300 K.<BR>
> > > > gen_vel = no<BR>
> > > > gen_temp = 300<BR>
> > > > gen_seed = 173529<BR>
> > > > ~<BR>
> > > ><BR>
> > > > Waiting
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