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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>>
>
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Received on Mon Nov 26 2018 - 13:00:02 PST
