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 Fri May 11 2018 - 23:30:02 PDT
