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 - 00:00:01 PDT
