Thomas E. Cheatham, Hi.
Thank you for your reply on TMD. I am a new one for amber, I think I should better say more detail about my project, could you give me a suggestion?
Now I have two conformation of a protein. I choosed one as initial conformation, added WATER216 within box(10.0 angstroms), minimized and increased temperature from 0K to 300K.
I put another conformation into the xleap for adding the same number of WATER216, and used it as a ref. RMSD between two conformations measured by spdbv is below 14 angstroms, but when I run the sander using parameters that I provided last time, it showed above 440 angstroms(maybe water was calculated, I don't know about it), thought I refined the group that only consist of protein atom in the parameter file.
I have seen some targeted MD examples provied in tgtmd directory, but I don't know that when I use the implicit solvent, How can I deal with explicit solvent that I added during the minimization and the process of increasing temperature(Should I delete them? or only perform minimization and increasing temperature without water?) Could you give me some tips of reasonable GB parameters with other conditions (PME and cutoff)?
I used 10000 step in order to test change on RMSD only from 442 to 440, it is not complete time for whole change, and dt=0.0005 is a sample from examples(I thought 0.002 may be suitable enough). I want to give more accurate non-bond interaction using larger cutoff.
I am suffering about this and very appreciated for you help. Thank you in advance
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> I have two conformations of a protein which have a RMSD of 440
> angstrom. I want to transfor from one conformation to another. In the
>Are you sure that the difference is 440 angstroms or 44 nm? If so this is
>of such an extremely large size that a few picoseconds (10000 * 0.0005 or
>5 ps) will not be sufficient to move the system at all. It is very
>unlikely that the system can adapt to such large force/structure changes
>(on the order of 400 angstroms) in such a short period of time.
> imin=0, nstlim=10000, dt=0.0005,
>Why do you need to have the timestep so short (using SHAKE); are their
>instabilities in the system to begin with?
> ntpr=10, scee=1.2, cut=25,
> igb=0, irest=1, nmropt=1,
>It appears that you are not using generalized Born (implicit solvent) yet
>you have a large cutoff and PME was not turned off (in the &ewald namelist
>setting use_pme=0 ?); this is a bit confusing. Do you want gas phase?
> itgtmd=1, tgtrmsd=0.0, tgtmdfrc=0.5,
> &end
> &wt
> TYPE='TGTRMSD', istep1 =1, istep2 = 1000,
> value1 = 441.2, value2 = 440.,
> &end
>400 angstroms is a really large number in the atomistic world of AMBER
>simulation...
> 2.And In the output file, I found the temperature increased from 300K to
> 320K during 10000 steps, the whole energy was increased from negative
> value to positive. is it right? 3.Should I use the Born model(igb=1) for
> targeted MD?
>Do you have solvent? If not, figure out carefully how to run a vacuum
>simulation. If you can afford it, run GB (or implicit solvent) and even
>better explicit solvent (which can be debated); however the size system
>you are investigating (if the 400 angstroms RMSd is correct) is really at
>the cutting edge of what is currently possible.
>To better your understanding of targeted MD and these simulation
>protocols, it may be advantageous to run a small system first to test
>things out; watch movies, plot the energies and values and see what is
>happening.
Feel free to ask the list for further advice as many, if they understand
your problem well, will provide excellent insight beyond my comments.
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Received on Wed Mar 09 2005 - 13:53:00 PST
