I only looked at the first of the output files. Some thoughts :
- you're using igb=1,which is quite old and not a good choice for modern
simulations
- your initial restraint energy is huge because your initial rmsd doesn't
match your target value. Your temperature is over 1,400 degrees. wouldn't
trust anything that happens after that.
- I don't really understand your atom masks. Alternating groups of residues
in the fit and rmsd masks doesn't look like what was going on in the movie
you sent before. I'm not sure people will be able to help you select the
right masks since they are so project specific, but be sure they make sense
to you.
On Fri, Nov 30, 2018, 4:22 AM M. Reza Ganjalikhany <ganjalikhany.gmail.com
wrote:
> Here are the links to the outputs:
> https://www.dropbox.com/s/lkytj6a70wpr5kc/tmd5.out?dl=0
> https://www.dropbox.com/s/webobxahghmchs2/tmd2.out?dl=0
> https://www.dropbox.com/s/x6ni7r1vxelextr/tmd.out?dl=0
>
>
> On Fri, Nov 30, 2018 at 2:08 AM Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > Can you send me the output file off list?
> > Carlos
> >
> > On Thu, Nov 29, 2018, 8:32 AM M. Reza Ganjalikhany <
> ganjalikhany.gmail.com
> > wrote:
> >
> > > Dear Carlos,
> > >
> > > As my structure has a large and complicated conformational change along
> > two
> > > axes, I am not sure whether TMD is enable of simulating such transition
> > in
> > > a low energy path or just move the structure to lower the RMSD value
> > > regardless of any other parameters.
> > >
> > > Both cases (ntr=1. restrantmask) and (ntr=0 and tgtfitmask) worked
> with a
> > > slight difference. The output shows it recognizes the masks as reported
> > > below:
> > >
> > > 5. REFERENCE ATOM COORDINATES
> > >
> > > defa
> > > Mask :1-114,131-166,188-204,229-249,448-577.CA; matches 318
> atoms
> > > Mask ":115-130,167-187,205-228,250-447,578-775.CA" matches 437
> > > atoms
> > >
> > > As you mentioned, I used cpptraj to see the changing in the RMSD value.
> > It
> > > decreased until the half and then it increased slowly as it could not
> > find
> > > the final position. The decrease is due to the movement of N-terminal
> > > domain to the reference structure but it should rotate to fit the
> target.
> > > It seems that the combination of these two movement is not possible at
> > the
> > > same time.
> > > Also, I have tested bigger force constants and the result was not
> really
> > > desirable as the structure denatured during the movement.
> > >
> > > Here are the links to some visualized trajectories:
> > > https://www.dropbox.com/s/weezo4c1hmoc68j/TMD1.mp4?dl=0
> > > https://www.dropbox.com/s/htjdlyuohlglxt5/TMD2.mp4?dl=0
> > > https://www.dropbox.com/s/j7idltd4ax0iaw1/TMD5.mp4?dl=0
> > >
> > > On Tue, Nov 27, 2018 at 12:24 AM Carlos Simmerling <
> > > carlos.simmerling.gmail.com> wrote:
> > >
> > > > also your force constant is really small
> > > >
> > > > On Mon, Nov 26, 2018 at 3:52 PM Carlos Simmerling <
> > > > carlos.simmerling.gmail.com> wrote:
> > > >
> > > > > see section 20.4 of the Amber18 manual - you should be using
> > tgtfitmask
> > > > > and tgtrmsmask but I only see tgtrmsmask in your input.
> > > > > I'm not sure what would happen when you also turn on positional
> > > > restraints
> > > > > as you have done here (using ntr=1 and restraintmask)- it might
> work,
> > > but
> > > > > it might not depending on how that matches the other masks. I don't
> > > have
> > > > > the ability to check the code right now.
> > > > > what does the beginning of the output say about the targeted md
> part?
> > > > does
> > > > > it give a fitmask?
> > > > >
> > > > > to check and see if it's working, the best way is to use cpptraj to
> > do
> > > > the
> > > > > rmsd fit to the same reference structure that you gave the md code,
> > > using
> > > > > the same mask as you use for tgtfitmask, and then calculate the
> rmsd
> > > next
> > > > > using the tgtrmsmask but including the "nofit" flag. The resulting
> > data
> > > > > stream should match what you asked the md to do (though it's
> unlikely
> > > > that
> > > > > it can reach exactly 0 rmsd).
> > > > >
> > > > >
> > > > > On Mon, Nov 26, 2018 at 3:22 PM M. Reza Ganjalikhany <
> > > > > ganjalikhany.gmail.com> wrote:
> > > > >
> > > > >> Dear Amber users,
> > > > >>
> > > > >> I am trying to run targeted MD to study a large conformational
> > change
> > > > >> during the simulation between two states of a protein. As I check
> > the
> > > > >> movies from the trajectories, I see that the structure moves from
> > > > initial
> > > > >> to the final structure, but it does not stop at the final point
> and
> > it
> > > > >> continues to move further beyond the final position. Also, the
> > moving
> > > > part
> > > > >> of the structure hits other parts of the protein and I realize
> that
> > > this
> > > > >> movement will not show the low energy path between the initial and
> > > final
> > > > >> conformations.
> > > > >> I have changed the parameters but I couldn't solve the problem.
> > Since
> > > I
> > > > >> performed short simulations to see the results quickly, I am not
> > sure
> > > > >> whether I have to set large number for *nstlim *or reduce the
> > *tgtfrc
> > > ?
> > > > >> *Is
> > > > >> there any other parameter which is neglected or should be defined
> in
> > > the
> > > > >> input file? The input file has been attached. I wanted to send the
> > > > movies
> > > > >> but it is not possible due to the limitation is the email size.
> > > > >>
> > > > >> I appreciate you valuable comment to tackle this problem.
> > > > >>
> > > > >> Regards,
> > > > >>
> > > > >> Input parameters for targeted MD:
> > > > >> TMD icl2
> > > > >> &cntrl
> > > > >> imin = 0, ntx = 1, nstlim = 12000, irest=0, dt = 0.002, ntc = 2,
> > > ntf =
> > > > >> 2,
> > > > >> tol = 0.000001, tempi = 100.0, temp0 = 300.0, cut = 10.0,
> > > > >> ntpr = 10, ntwx = 10, ntwr = 100, ntb = 0, ntt = 1, tautp = 0.5,
> > > ntp =
> > > > >> 0,
> > > > >> igb = 1, nscm = 0, nmropt = 1, ntr = 1, restraint_wt=0.02,
> > > > >> itgtmd = 1, tgtrmsd = 39.553, tgtmdfrc = 0.005, restraintmask=
> > > > >> ":1-114,131-166,188-204,229-249,448-577.CA"
> > > > >> tgtrmsmask= ":115-130,167-187,205-228,250-447,578-775.CA",
> > > > >> /
> > > > >> &wt
> > > > >> TYPE='TGTRMSD', istep1=1, istep2=8000,
> > > > >> value1 = 0.0500, value2 = 0.0,
> > > > >> /
> > > > >> &wt
> > > > >> TYPE='TGTRMSD', istep1=8000, istep2=12000,
> > > > >> value1 = 0.0, value2 = 0.0,
> > > > >> /
> > > > >> &wt
> > > > >> type="END",
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Received on Fri Nov 30 2018 - 04:30:01 PST
