Hi Matthew,
I think you are right: the manual description is not accurate. Anyway, you should set beta=50 Å^2 if gti_lam_sch=1 or 1.0 if gti_scale_beta=1.
When you look into source code, you also need to look at the GTI compilation flag at the same time. The scbeta=12 in line 826 is for CPU. "Reset to -100" is to indicate there is no user input value so that it can be reset later (for GPU only). gti_auto_alpha is an experimental thing and not for users to modify at this point.
Best,
Taisung
-----Original Message-----
From: Matthew Guberman-Pfeffer <matthew.guberman-pfeffer.uconn.edu>
Sent: Saturday, November 26, 2022 1:37 AM
To: Matthew Guberman-Pfeffer <matthew.guberman-pfeffer.uconn.edu>; AMBER Mailing List <amber.ambermd.org>; accuratefreeenergy.gmail.com
Subject: Re: {SPAM?} [AMBER] scbeta, wrong default?
Adding more details:
In mdin_ctrl_dat.F90 scbeta is set to 12.0 on line 826. Then reset to -100.000 on line 873. An if-loop starting on line 3517 then sets the .lt. 0 sets scbeta to 4.0 if gti_auto_alpha is .gt. 0 or else sets it to 12.0. What gti_auto_alpha does is not described in the manual or the source code so far as I can tell.
The above doesn't seem consistent with the manual that says scbeta is set to 50 Å^2 if gti_lam_sch=1 or 1.0 if gti_scale_beta=1. Why do the manual and the source code give different defaults for scbeta (and scalpha, by the way)? What values should I use?
Obviously, since I’m looking at source code at nearly 2 AM, this is really important for me to figure out. Can anyone please help?
Best,
Matthew
> On Nov 25, 2022, at 7:15 PM, Matthew Guberman-Pfeffer via AMBER <amber.ambermd.org> wrote:
>
> *Message sent from a system outside of UConn.*
>
>
> Dear AMBER community,
>
> When I set gti_scale_beta=1, I see in the output scbeta=12 in the below output, but the manual says the default is 1.0. What should it be?
>
> Input:
> &cntrl
> ig=-1,
> irest=0, ntx=1,
> dt=0.001, nstlim=10000000,
> ntt=3, gamma_ln=2.0, tempi=300.0, temp0=300.0, ntb=2, ntp=1,
> barostat=2, pres0=1.0, taup=1.0, igb=0, cut=10.0, ntc=2, ntf=1,
> ntr=0, nmropt=1,
>
> icfe=1, klambda=1,
> clambda=0.0, dynlmb=0.000000, ntave=125000, tishake=1,
> noshakemask=':255,564,309,618', timask1=':255,564',
> timask2=':309,618',
> scmask1='(:255&.CB,HB2,HB3,CG,HG2,HG3,CD,OE1,OE2)|(:564&@CB,HB2,HB3,CG
> ,HG2,HG
> scmask2='(:309&@CB,HB2,HB3,CG,HG2,HG3,CD,HD2,HD3,CE,HE2,HE3,NZ,HZ1,HZ2
> ,HZ3)|(
> gti_syn_mass=0,
> crgmask= ,
> ti_vdw_mask= ,
>
> ifsc=1, gti_lam_sch=1,
> gti_scale_beta=1,
> !scalpha=0.5, scbeta=1.0, ! default
> gti_ele_exp=2, gti_vdw_exp=6 ! default gti_ele_sc=1, gti_vdw_sc=1,
> ! default
> gti_cut=1, ! Default
> gti_cut_sc=2,
> gti_chg_keep=1, ! default
> gti_add_sc=1, gti_bat_sc=0, ! default
>
> ioutfm=1, iwrap=0,
> ntwr=10000, ntwx=10000, ntpr=10000, ntxo=2, logdvdl=1, gti_output=1,
> gti_cpu_output=1, / &wt type='DUMPFREQ', istep1=1000 / &wt type='END'
> / DISANG=InterSubunitRestraints.rst
> DUMPAVE=InterSubunitRestraints_TIprep.dat
>
> Output:
> ….
> Free energy options:
> icfe = 1, ifsc = 1, klambda = 1
> clambda = 0.0000, scalpha = 0.5000, scbeta = 12.0000
> sceeorder = 2
> dynlmb = 0.0000 logdvdl = 1
> ….
>
>
> Best,
> Matthew
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists
> .ambermd.org%2Fmailman%2Flistinfo%2Famber&data=05%7C01%7C%7C9cd623
> b4e86840b6f8c708dacf437f96%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%
> 7C638050186062284576%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQI
> joiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=G8
> mUY85Bh%2BFlFhDJgULv5ufAQ39sqUjQ1XD%2BiOy4LSM%3D&reserved=0
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Nov 28 2022 - 07:00:03 PST
