[gmx-users] why protein comes out of the box

[Erik Marklund]

7 feb 2007 kl. 12.48 skrev sangeeta kundu:

> Dear Sir,
>
>     I am facing one  problem, I gave the MD run of a protein of  
> approximately 70 residues for 10ns, after 1 ns run part of protein  
> was getting out of the waterbox and at the end of 10 ns I found  
> that almost half of the protein was coming out of the waterbox, I  
> gave the simulation under NPT condition at 46C and 1BAR pressure, I  
> used  43a1 force field and spc water.

Why would this be a problem? Proteins do diffuse you know. And since  
you have pbc the protein cannot really leave the waterbox.

/Erik

>
> This is my md.mdp file
>
>  title               =  Yo
> cpp                 =  /usr/bin/cpp
> constraints         =  all-bonds
> integrator          =  md
> dt                  =  0.002    ; ps !
> nsteps              =  5000000  ; total 10 ns.
> nstcomm             =  1
> nstxout             =  250
> nstvout             =  1000
> nstfout             =  0
> nstlog              =  100
> nstenergy           =  100
> nstlist             =  10
> ns_type             =  grid
> pbc                 =  xyz
> coulombtype         =  PME
> rlist               =  0.9
> rcoulomb            =  0.9
> rvdw                =  0.9
> fourierspacing      =  0.12
> pme_order           =  4
> ewald_rtol          =  1e-5
> ; Berendsen temperature coupling is on in two groups
> Tcoupl              =  berendsen
> tc-grps             =  Protein  SOL
> tau_t               =  0.1      0.1
> ref_t               =  319      319
> ; Energy monitoring
> energygrps          =  Protein  SOL
> ; 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            =  319.0
> gen_seed            =  173529
> I used the 43a1 force field, and prepared the water box by the  
> commands
> editconf -bt triclinic -f conf.pdb -o box.pdb -c -d 1.0
> genbox -cp box.pdb -cs spc216 -o water.pdb -p topol.top
>
> But I wonder that  while executing the command
> grompp -f em.mdp -c water.pdb -p topol.top -o em.tpr
>
> it did not display any charge , so I did not add any counterion to  
> my protein, in the subsequent steps em.pdb and pr.mdp files were  
> produced and in both the cases the protein was almost in  the  
> centre of the box, while I took the snapshot after 1ns the protein  
> was still at the centre , but after 1 ns it was coming to one  
> corner of the box, and finally almost half of it was outside the  
> box when I completed the run, I can not detect why it is coming  
> outside the box?
>
> Where am I doing mistake? Another question is how can I understand  
> that the simulation has been completed successfully?
> Please help.
> regards
> SANGEETA
>
>
>
>
>
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_______________________________________________
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,	75124 Uppsala, Sweden
phone:	+46 18 471 4537		fax: +46 18 511 755
erikm at xray.bmc.uu.se	http://xray.bmc.uu.se/molbiophys


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