[gmx-users] RMSD plot

[Florian Haberl]

Hi,

On Thursday, 15. May 2008 18:04, Justin A. Lemkul wrote:
> 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.


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 <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/
>
> ========================================
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-- 
-------------------------------------------------------------------------------
 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
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