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 - 13:30:04 PDT
