Hi Adrian and Zhuoran,
As the implementer of this keyword, my answer:
1. If you have odd-number of replicas, you can NOT do exchange between the first and the last, or you will leave one middle replica alone without doing exchange.
2. Although the exchange between the first and the last replicas seems not a big deal--theoretically, sometimes it will give troubles in TI calculations: you need to evaluate the potential energy based on the Hamiltonian of the first replica with the conformation of the last replica--such calculations could lead GPU overflows and crash the simulation. In fact, this was the main reason I implemented this keyword to prevent the exchange between the first and the last.
Taisung
-----Original Message-----
From: Adrian Roitberg via AMBER <amber.ambermd.org>
Sent: Tuesday, August 16, 2022 11:44 AM
To: Zhuoran Long <zl1277.nyu.edu>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] gremd_acyc keyword for H-REMD
Yes, you are right, that is what that keyword is supposed to do.
However, if you do not use it, the only thing that happens is that the remd will try to exchange the first and last replicas, as you mentioned.
If they are too far apart, they will "never" exchange, which is the correct behavior.
Bottom-line, there is nothing to gain from using it if you have an even number of replicas.
adrian
On 8/15/22 4:42 PM, Zhuoran Long wrote:
> *[External Email]*
>
> 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
> <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdisang_cocc_001.in%2F&data=05%7C01%7Croitberg%40ufl.edu%7C69d8c9334abc498ce99408da7efeb8d9%7C0d4da0f84a314d76ace60a62331e1b84%7C0%7C0%7C637961929800309591%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ljdxwGn2r1JB9u%2B2LMRRmVBegr%2FAtbmLhLoRIuQBM5I%3D&reserved=0>
> > 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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--
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 Tue Aug 16 2022 - 20:00:05 PDT
