It sounds like you are better off running your simulation to get initial
structures using an NVT rather than NpT protocol. You probably have to
re-equilibrate anyway once the box changes, as this will induce artifacts
at the edges.
Or am I missing something here?
Brian
On Tue, Aug 26, 2014 at 2:35 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Tue, Aug 26, 2014 at 11:58 AM, George Green <soyo.green.gmail.com>
> wrote:
> > 3) Initially I was attempting to use cpptraj to try and put the box in.
> > However, I realised that Jason has a helpful script called
> > get_restarts.py that outputs restart files from the initial trajectory. I
>
> Out of curiosity, why couldn't you use cpptraj for this? If there is
> box info in the input trajectory that box info will be in the output
> restart file (as long as 'nobox' is not specified to 'trajout').
>
> -Dan
>
> > opted to use this and manually modified the box information on the last
> > line to match that of the parameter file used in step1.
> >
> > 4) However, now I have a problem during minimisation which tends to stall
> > and quit for some of the restart files that form the basis of the various
> > US windows. I am currently trying to employ a more gentle two step
> > minimisation to try and avoid the minimiser stopping:
> >
> > ####################
> > step1 minimisation - hold all atoms with weak force
> > &cntrl
> > imin=1, ntmin=1, maxcyc=350, ncyc=200,
> > ntb=1, ntpr=5, ntwr=100000, drms=0.05,
> > cut=12.0, ntxo=2, ioutfm=1, NTR=1,
> > ntc=1, ntf=1,
> > ntb=1, ntp=0,
> > &end
> > Group input for restrained atoms
> > 0.5
> > RES 1 8866
> > END
> > END
> > ###################
> >
> > Then:
> >
> > ####################
> > step2 minimisation - unrestrained min
> > &cntrl
> > imin=1, ntmin=1, maxcyc=350, ncyc=200,
> > ntb=1, ntpr=5, ntwr=100000, drms=0.05,
> > cut=12.0, ntxo=2, ioutfm=1,
> > ntc=1, ntf=1,
> > ntb=1, ntp=0,
> > &end
> > &wt
> > type='END',
> > &end
> > DISANG=restraint_list_${frame}.dist
> > ###################
> >
> >
> > I'm hoping that you might have some suggestions regarding a better
> > minimsation protocol, or alternatively a better way to create the inpcrds
> > for umbrella sampling?
> >
> > Many thanks.
> >
> >
> >
> >
> >
> >
> >
> >
> > On Fri, Aug 22, 2014 at 6:54 PM, David A Case <case.biomaps.rutgers.edu>
> > wrote:
> >
> >> On Fri, Aug 22, 2014, George Green wrote:
> >> >
> >> > Thanks for pointing that out. I changed the script to the following
> and
> >> it
> >> > now seems to work at the equilibration stage.
> >> >
> >> > ###############
> >> > source leaprc.gaff
> >> > source leaprc.ff99SBnmr
> >> > loadAmberParams frcmod.tip4pew
> >> > loadoff doc_final.lib
> >> > mol = loadpdb frame5_tryUS.pdb
> >> > charge mol
> >> > setBox vdw mol centers
> >>
> >> I doubt that this is what you really want. If you know the "correct"
> box
> >> sizes, use the "set <unit> box ...." command.
> >>
> >> Apologies if I am not really understanding your workflow.
> >>
> >> ...regards...dac
> >>
> >>
> >> _______________________________________________
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> >>
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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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>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
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Integrative Proteomics Room 308
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Received on Tue Aug 26 2014 - 12:00:03 PDT
