[gmx-users] vacuum simulation problem
Gerrit Groenhof (RUG)
g.groenhof at rug.nl
Wed Aug 9 10:44:40 CEST 2006
In addition to Erik and my suggestions, you should also remove the
overall rotation: comm_mode=linear.
anwar at cdfd.org.in wrote:
>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.
>; 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.
>Lab of Computational Biology and Bioinformatics
>Center for DNA Fingerprinting and Diagnostics(CDFD)
>Tel: +91-8413-235467,68,69,70 ext 2019
>anwar.m1 at gmail.com
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