I don't think that input makes sense to me. If the tgtmdfrc is at zero,
there is no point to making changes in tgtrmsd.
On Mon, May 14, 2018, 2:44 AM Aravind Ravichandran <raravind.ibab.ac.in>
wrote:
> Thanks Carlos, for the reply. Regarding my second question, since I want
> to equilibrate the system along with TMD, id it possible control TGTMDFRC
> variable and change it during TMD, as I have shown in my input file?
>
> Thanks,
> Aravind R
>
> > Yes setting the force constant to zero will not change the structure. The
> > calculations will be slower though, so I recommend turning off this
> > feature
> > if you don't use non zero force constant. There is no point to having the
> > tgtrmsd set if you have zero force constant.
> >
> > On Sat, May 12, 2018, 2:26 AM Aravind Ravichandran <raravind.ibab.ac.in>
> > wrote:
> >
> >> Dear all,
> >> I am trying to simulate a protein from its open conformation to close
> >> conformation. I am using TMD for this. I want this simulation to be as
> >> close as possible to normal MD and therefore I would like to equilibrate
> >> the structure, along TMD. I have couple of questions regarding the same.
> >>
> >> 1) Does setting TGTMDFRC to 0 means that we are doing the normal NPT
> >> simulation, with RMSD calculated on the run?
> >> (Because, when I performed TMD with tgtmdfrc 0, my RMSD increased rather
> >> than decreasing(moving away from the target)).
> >>
> >> 2)I wanted to know if it is possible to use NMR restraints option to
> >> gain
> >> control over multiple parameters during a single simulation?
> >> (For example,
> >> my input is,
> >> Ubi targeted MD
> >> &cntrl
> >> imin = 0, nstlim = 1000000, dt = 0.002,
> >> ntx = 1, ntt = 3, gamma_ln = 1.0,
> >> ntc = 2, ntf = 2, ntb = 2, ntp=1,
> >> cut = 10.0, nscm = 0,
> >> ntpr = 500, ntwx = 1000, ntwr = 1000,
> >> igb = 0, irest=0, nmropt=1,tempi=300.0,
> >> itgtmd=1, tgtmdfrc=0.001,
> >> tgtfitmask=":77-222.CA,N,C,O",
> >> tgtrmsmask=":1-70.CA,N,C,O",
> >> /
> >> &wt
> >> TYPE='TGTRMSD', istep1 =1, istep2 = 80000,
> >> value1 = 37.417, value2 = 35.0,
> >> /
> >> &wt
> >> TYPE='TGTRMSD', istep1 =80001, istep2 = 120000,
> >> value1 = 35.0, value2 = 35.0,
> >> /
> >> &wt
> >> TYPE='TGTRMSD', istep1 =120001, istep2 = 200000,
> >> value1 = 35.0, value2 = 30.0,
> >> /
> >> &wt
> >> TYPE='TGTRMSD', istep1 =200001, istep2 = 240000,
> >> value1 = 30.0, value2 = 30.0,
> >> /
> >> &wt
> >> TYPE='TGTRMSD', istep1 =240001, istep2 = 320000,
> >> value1 = 30.0, value2 = 25.0,
> %
>
>
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Received on Mon May 14 2018 - 05:30:04 PDT
