[gmx-users] vacuum simulation problem

[Gerrit Groenhof (RUG)]

In addition to Erik and my suggestions, you should also remove the 
overall rotation: comm_mode=linear.

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. 
>;       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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