[gmx-users] invacuo minimization

[David van der Spoel]

anwar at cdfd.org.in wrote:
> Dear gmx users,
> When I am minimizing a trimer protein in vacuum by SD as well as CG methods, 
> one of the monomer gets apart from the rest of the protein and places itself 
> away from the other two monomers, which are intact. No periodic box is 
> assigned. But when I am running editconf and assigning a box, then the 
> structures are intact. What is the reason for the above behaviour? 
> I am pasting the em.mdp below:

chekc your mdout.dmp, the default pbc = xyz

> 
> cpp                 =  /lib/cpp
> define              =  -DFLEX_SPC
> constraints         =  none
> ;integrator          =  CG
> integrator          =  steep
> nsteps              =  1000
> ;
> ;       Energy minimizing stuff
> ;
> emtol               =  100
> ;for SD
> emstep              =  0.1
> ;for CG
> ;emstep              =  0.001
> 
> nstcomm             =  1
> ns_type             =  grid
> rlist               =  1
> rcoulomb            =  1.0
> rvdw                =  1.0
> Tcoupl              =  no
> Pcoupl              =  no
> gen_vel             =  no
> 
> 
> 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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