[gmx-users] Vacuum simulation problem

[Erik Marklund]

The loop probably allows the two domains to move a lot in respect to
each other. Have you tried using only one domain for both superposition
and RMSD calculation? Doing just that for both domains, one after
another, should give you a hint about whether the two domains are sort
of intact, but moving, or if the structural change actually occurs
within the two domains.

/Erik

On Wed, 2006-08-09 at 05:16 -0700, anwar at cdfd.org.in wrote:
> Dear all,
> I am simulating a protein containing 2 domains which are linked together 
> by a loop of around 10 residues. When I am simulating the same in vacuum, 
> after approx 1ns, the rmsd has increased from 5 angstroms to 25 angstroms 
> with in 10 time steps. You can surely imagine how drastic the structural 
> changes are happening. 
> What exactly might be happening there, why the protein is behaving like 
> that. I am pasting the mdp file below. 
> ;       User spoel (236)
> ;       Wed Nov  3 17:12:44 1993
> ;       Input file
> ;
> title               =  Yo
> cpp                 =  /lib/cpp
> constraints         =  all-bonds
> ;define              =  -DPOSRES
> integrator          =  md
> dt                  =  0.002    ; ps !
> nsteps              =  10000000 ; total 10000 ps.
> nstcomm             =  1
> nstxout             =  500
> nstvout             =  500
> nstfout             =  500
> nstlog              =  500
> nstenergy           =  500
> nstlist             =  10
> ns_type             =  grid
> rlist               =  0.9
> rcoulomb            =  0.9
> rvdw                =  0.9
> ; Berendsen temperature coupling is on in two groups
> Tcoupl              =  berendsen
> tc-grps             =  Protein
> tau_t               =  0.1
> ref_t               =  300
> ; Energy monitoring
> energygrps          =  Protein
> ; Isotropic pressure coupling is now on
> Pcoupl              =  berendsen
> Pcoupltype          = isotropic
> tau_p               =  0.5
> compressibility     =  4.5e-5
> ref_p               =  1.0
> ; Generate velocites is off at 300 K.
> gen_vel             =  no
> gen_temp            =  300.0
> gen_seed            =  173529
> 
> 
> kindly guide me in this issue.
> regards
> Anwar
> 
> ----------------------
> Mohd Anwaruddin
> Project Assistant
> C/o DR.H.A.Nagarajaram
> Lab of Computational Biology and Bioinformatics
> Center for DNA Fingerprinting and Diagnostics(CDFD)
> Nacharam
> Hyderabad-500 076
> INDIA.
> Tel: +91-8413-235467,68,69,70 ext 2019
> anwar.m1 at gmail.com
> -----------------------
> 
> 
> 
> -
> 
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-- 
Erik Marklund, PhD Student, Molecular Biopcysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone: +46 18 471 4537          fax: +46 18 511 755
erikm at xray.bmc.uu.se