[gmx-users] why protein comes out of the box
Erik Marklund
erikm at xray.bmc.uu.se
Wed Feb 7 13:34:15 CET 2007
I'd say the mdp looks fine, after a quick glace at it.
Didn't pdb2gmx give you information about the charge state of the
protein? There is a bunch of papers out there assessing the
importance of ions in simulations of both neutral and charged
solutes. It will depend on your protein and the scientific question
you intend to investigate.
As Mark mentioned, a general answer to wether the a simulation is
"correct" is hard to give. I suggest to have a look at the energies,
temperatures and structures from the simulation to begin with. It
might give away flaws in the system preparation or simulation
parameters.
/Erik
7 feb 2007 kl. 13.24 skrev sangeeta kundu:
> Dear Sir,
>
> Thanks for your prompt reply, It seems that we do not have to
> bother about whether the protein is coming out of the box or not as
> already we introduced pbc? Then how should we understand that the
> simulation is correct?
> Will you please kindly check over my md.mdp file, Another
> trouble I was facing that when running grompp it did not give any
> information about charge, previously when I ran the same for other
> proteins it always gave information about charge, so I had to add
> counter ion , but here I did not. Am I doing any mistake?
> Please help.
>
> regards
> SANGEETA
>
>
> Erik Marklund <erikm at xray.bmc.uu.se> wrote:
>
> 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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_______________________________________________
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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