Dear Dan
I have a question on production input file of Ankinta related to "nmr
restraints"
Some how in my case I have to use NMR restraints during MD simulation in
explicit solvent.
I haven't yet found a correct method to use restraints during MD.
I was previously using same file as Ankita (script below)
&wt type='REST', istep1=1,istep2=5000000,
value1=1.0,value2=1.0, /
Instead of above script I have changed the following script (to increase
and gradually decrease nmr restraints weight)
&wt type='REST', istep1=1,istep2=1000000,
value1=0.0,value2=1.0, /
&wt type='REST', istep1=1000001,istep2=4000000,
value1=1.0, value2=1.0 /
&wt type='REST', istep1=4000001,istep2=5000000,
value1=1.0, value2=0.0 /
In Ankita case NMR restraints are on during entire MD, so my question is
which is correct method when it comes
to using NMR restraints in MD simulation (tip3pbox). They should be active
whole MD time or do we have to remove restraints
gradually during MD. I have got mixed answer from the forum it confused me.
I would be very happy to receive your suggestions.
thanks in advance...
Vince
On Thu, May 26, 2016 at 8:30 AM, ankita mehta <mehtaroadies.gmail.com>
wrote:
> Yup!
> Thanks!
>
> On Thu, May 26, 2016 at 2:25 AM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>
> > On Tue, May 24, 2016 at 11:57 PM, ankita mehta <mehtaroadies.gmail.com>
> > wrote:
> > > Same trouble i experienced in the .mdcrd file . but i processed them in
> > > cpptraj using following:
> > > parm model3.prmtop
> > > trajin modelprod5.rst
> > > image center
> > > trajout modelprod5new.rst
> > > go
> > > quit
> > >
> > >
> > > But i dont know the way to process the .rst file?
> >
> > Just write out a PDB instead of a restart.
> >
> > trajout modelprod5new.pdb
> >
> > -Dan
> >
> > >
> > > Can anyone guide ?
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> >
> >
> > --
> > -------------------------
> > Daniel R. Roe, PhD
> > Department of Medicinal Chemistry
> > University of Utah
> > 30 South 2000 East, Room 307
> > Salt Lake City, UT 84112-5820
> > http://home.chpc.utah.edu/~cheatham/
> > (801) 587-9652
> > (801) 585-6208 (Fax)
> >
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Received on Thu May 26 2016 - 02:30:03 PDT
