[gmx-users] vacuum simulation problem

[David van der Spoel]

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. And also during the simulation after 500ps the protein 
> started to rotate and later at approx 2ns the protein stopped rotation. 
> What exactly might be happening there, why the protein is behaving like 
> that. I am pasting the mdp file below. 

As Gerrit said, remove pressure coupling in vacuo and remove angular 
center of mass motion.


> ;       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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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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