[gmx-users] Vacuum simulation problem

[Gerrit Groenhof (RUG)]

Do not use Pressure coupling in vacuo. ALso you seem to be running with 
periodic boundary conditions. Switch that off as well and use ns_type = 
simple, and finally use infinite cut-offs when simulating in vacuo. qa 
cut-off of 0.9 is way too short. If you think the lack of water causes 
the conformatational changes and you don't want that, you can try 
putting position restraints on backboneatoms of solvent exposed residues.

Gerrit



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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