Hi Adrian,
The md can run after removing the gremd_acyc keyword. However it involving
exchange between the first and last replicas. In my case, the
generalized distance reaction coordinates are restrained to about -2
Angstrom and +2 Angstrom in these two replicas.
The amber 2021 manual says, " gremd_acyc (H-REMD only) When set to 1, the
exchange between the first and the last replicas will not be considered and
odd numbers of replicas are allowed. Default: 0". That's why I want to use
this keyword.
Thank you,
Zhuoran
Adrian Roitberg via AMBER <amber.ambermd.org> 于2022年8月15日周一 16:01写道：
> Hi
>
> As far as I know, that keyword has nothing to do with periodicity. It is
> there to enable an odd number of replicas, instead of the usual even_number
>
> So, try to use an even number of replicas without gremd_acyc=1 and see
> what happens.
>
> adrian
>
>
> On 8/15/22 3:48 PM, Zhuoran Long via AMBER wrote:
> > [External Email]
> >
> > Hi,
> >
> > I‘m trying to use the H-REMD for umbrella sampling. I'm using a
> generalized
> > distance reaction coordinate, which is not periodic. Therefore I tried
> the
> > gremd_acyc keyword. However, it gives the "error in reading namelist
> cntrl"
> > using sander.MPI and amber version 20.11. This error disappears when not
> > including this keyword. I also tried version 20.06 and 22.00 but neither
> > version works. I need to use the semiempirical QM/MM so I can't switch to
> > pmemd.MPI.
> > I notice that this keyword is introduced in Sept 2019. I can't find any
> > examples including the amber test codes.
> > I paste my input file below. Any suggestions or examples are appreciated.
> >
> > Best,
> > Zhuoran
> >
> > HREMD-Umbrella sampling
> > &cntrl
> > imin = 0,
> > irest = 1,
> > iwrap = 1,
> > ntx = 5,
> > ntxo= 1,
> > nstlim= 100,
> > dt = 0.001,
> > ntc = 1,
> > ntf = 1,
> > cut = 8,
> > ntb = 2,
> > ntp = 1,
> > pres0 = 1.0,
> > taup= 5.0,
> > ntpr= 500,
> > ntwx= 500,
> > ntt = 3,
> > gamma_ln = 1.0,
> > temp0 = 300.0,
> > ioutfm= 1,
> > ifqnt = 1,
> > nmropt= 1,
> > ig = 4746,
> > numexchg = 5,
> > gremd_acyc=1
> > /
> > &qmmm
> > qmmask=':1',
> > qmcharge=-2,
> > qm_theory='PM3',
> > qmshake=1,
> > qm_ewald=1, qm_pme=1,
> > /
> > &wt
> > type='DUMPFREQ', istep1=500,
> > /
> > &wt
> > type='END',
> > /
> > DISANG=disang_cocc_001.in
> > DUMPAVE=cocc_001.dat
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> --
> Dr. Adrian E. Roitberg (he/him/el)
> V.T. and Louise Jackson Professor in Chemistry
> Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
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Received on Mon Aug 15 2022 - 14:00:03 PDT
