[gmx-users] RMSD plot

[Justin A. Lemkul]

Quoting minnale <minnale_gnos at rediffmail.com>:

>
> 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.

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 <minnale_gnos at rediffmail.com>:
> >
> > >
> > > 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
> >jalemkul at vt.edu | (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
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

========================================