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,
> /
> &wt
> TYPE='TGTRMSD', istep1 =320001, istep2 = 360000,
> value1 = 25.0, value2 = 25.0,
> /
> &wt
> TYPE='TGTRMSD', istep1 =360001, istep2 = 440000,
> value1 = 25.0, value2 = 20.0,
> /
> &wt
> TYPE='TGTRMSD', istep1 =440001, istep2 = 480000,
> value1 = 20.0, value2 = 20.0,
> /
> &wt
> TYPE='TGTRMSD', istep1 =480001, istep2 = 560000,
> value1 = 20.0, value2 = 15.0,
> /
> &wt
> TYPE='TGTRMSD', istep1 =560001, istep2 = 600000,
> value1 = 15.0, value2 = 15.0,
> /
> &wt
> TYPE='TGTRMSD', istep1 =600001, istep2 = 680000,
> value1 = 15.0, value2 = 10.0,
> /
> &wt
> TYPE='TGTRMSD', istep1 =680001, istep2 = 720000,
> value1 = 10.0, value2 = 10.0,
> /
> &wt
> TYPE='TGTRMSD', istep1 =720001, istep2 = 800000,
> value1 = 10.0, value2 = 5.0,
> /
> &wt
> TYPE='TGTRMSD', istep1 =800001, istep2 = 840000,
> value1 = 5.0, value2 = 5.0,
> /
> &wt
> TYPE='TGTRMSD', istep1 =840001, istep2 = 920000,
> value1 = 5.0, value2 = 0.0,
> /
> &wt
> TYPE='TGTRMSD', istep1 =920001, istep2 = 1000000,
> value1 = 0.0, value2 = 0.0,
> /
> &wt
> TYPE='TGTMDFRC', istep1 =80001, istep2 = 120000,
> value1 = 0.0, value2 = 0.0,
> /
> &wt
> TYPE='TGTMDFRC', istep1 =200001, istep2 = 240000,
> value1 = 0.0, value2 = 0.0,
> /
> &wt
> TYPE='TGTMDFRC', istep1 =320001, istep2 = 360000,
> value1 = 0.0, value2 = 0.0,
> /
> &wt
> TYPE='TGTMDFRC', istep1 =440001, istep2 = 480000,
> value1 = 0.0, value2 = 0.0,
> /
> &wt
> TYPE='TGTMDFRC', istep1 =560001, istep2 = 600000,
> value1 = 0.0, value2 = 0.0,
> /
> &wt
> TYPE='TGTMDFRC', istep1 =680001, istep2 = 720000,
> value1 = 0.0, value2 = 0.0,
> /
> &wt
> TYPE='TGTMDFRC', istep1 =800001, istep2 = 840000,
> value1 = 0.0, value2 = 0.0,
> /
> &wt
> TYPE='TGTMDFRC', istep1 =920001, istep2 = 1000000,
> value1 = 0.0, value2 = 0.0,
> /
> &wt
> type="END",
> /
> where I control RMSD along simulation, and the steps where I have kept the
> RMSD to be same and not change over time, I want the TGTMDFRC to be 0, so
> that it samples more structures without any for constraint and
> equilibrate, whereas during the steps where RMSD reduces, I want the
> TGTMDFRC to be 0.001.
>
> Thanks in advance !
>
> With Regards,
> Aravind R
> Junior Research Fellow,
> National Center For Biological Sciences,
> Bangalore, India
>
>
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Received on Sat May 12 2018 - 11:00:03 PDT
