Have you previously used tmd and gotten output? For this system? Have you
run md and gotten output? It would help troubleshoot if we knew more.
Unrelated to the output file, I am not confident that the calculation you
have in your mdin will succeed. Going from 11.7 rmsd to 0 in 20ns is a huge
sampling problem, and the tmd doesn't really solve that. You're very likely
to create a compact misfolded structure along the way that cannot be
further improved due to clashes, but the restraints won't allow it to
unfold. For example, there are many 5A rmsd structures, but not all of them
can be turned into 0A structures without the rmsd going up first.
On Mar 4, 2015 5:44 AM, "Pallavi Mohanty" <pallavipmohanty.gmail.com> wrote:
> Hello Users,
> I have come across a weird problem. I am running TMD for 10ns wherein the
> rms difference between both the structure is 11.7 Å. Here is my input file
> &cntrl
>
> imin=0, ntx=5, nstlim=5000000,
> irest=1,
> dt=0.002, ntc=2, ntf=2,
> tol=0.000001,
>
> temp0=300.0,
> ntpr=5000, ntwr=5000,
> ntwx=5000,
> ntb=0, ntt=1, tautp=0.5,
> ntp=0,
>
> cut=16.0,
> igb=1, nscm=0,
> nmropt=1,
> itgtmd=1, tgtrmsd=11.7,
> tgtmdfrc=1.0,
> tgtfitmask=":1-30.CA,N,C,O",
>
> tgtrmsmask=":1-30.CA,N,C,O",
>
>
> /
>
> &wt
>
> TYPE='TGTRMSD', istep1=1, istep2=4000000, value1=11.7, value2=0.0,
> /
> &wt
>
> TYPE='TGTRMSD', istep1=4000000, istep2=5000000, value1=0.0, value2=0.0,
> /
> &wt
>
>
> type='END'
>
> /
>
> Though the run is successfully updating the mdcrd and mdinfo file but the
> out file is blank. What can be the possible cause?
>
> --
> Regards,
>
> Pallavi Mohanty
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Received on Wed Mar 04 2015 - 04:30:03 PST
