[gmx-users] (no subject)

[Justin A. Lemkul]

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/

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