Re: [GaMD-discuss] pyreweighting

[Miao, Y. <Yin...@me...>]

Hi,

You may use the latest PyReweighting scripts for the calculations: https://www.med.unc.edu/pharm/miaolab/resources/pyreweighting/

Also you want to make sure the number of data points in your data file (psi.dat) and weights.dat match each other.

Best,

Yinglong Miao, Ph.D.
Associate Professor
Computational Medicine Program and
Department of Pharmacology
University of North Carolina - Chapel Hill
Tel: 1-919-962-5696
http://miaolab.org

On Feb 14, 2024, at 6:04 AM, Emmanuel Bettler <emm...@ib...> wrote:

You don't often get email from emm...@ib.... Learn why this is important<https://aka.ms/LearnAboutSenderIdentification>
Hello,
i did a 100ns ppi-GaMD run for testing, using Amber22 and the following input file:
&cntrl
     imin=0,    irest=1,     ntx=5,
     nmropt=0,  iwrap = 0,
     ntt=1,     temp0=300.0, tautp=1,
     ntp=1,     taup=2.0,    ntxo=2,
     ntb=2,     ntc=2,       ntf=2,
     nstlim=100000000,          dt=0.002,
     ntwr=10000,  ntwx=100000,    ntpr=1000,

     icfe = 1,  ifsc = 1, gti_cpu_output = 0,
     gti_add_sc = 1,  timask1 = '',  scmask1 = '',
     bgpro2atm=2765,   edpro2atm=5788,   timask2 = '',
     scmask2 = '',
     igamd = 17,  iE = 1,  iEP = 1,  iED = 1,
     irest_gamd = 1,  ntcmd = 1000000,    nteb = 1000000,
     ntave = 50000,  ntcmdprep = 200000,  ntebprep = 200000,
     sigma0P = 6.0,  sigma0D = 6.0,
/
&wt type='END' /

For pyreweighting, i used cpptraj input file:
parm xxxx.prmtop
trajin xxxx_gamd.nc
check @C,N,O,CA,CB skipbadframes silent
dihedral phi :1@C :2@N :2@CA :2@C out phi.dat
dihedral psi :2@N :2@CA :2@C :3@N out psi.dat
run

and following run.sh script for weights.dat file.
When i run python command:
python PyReweighting-1D.py -input ./job0/psi.dat -cutoff 10 -Xdim -180 180 -disc 6 -Emax 20 -job amdweight_CE -weight weights.dat | tee -a reweight_variable.log
i've the error message:
DATA LOADED:    psi.dat
Effective acceleration factor with Gaussian approximation:  21381213.956709098
dV all: avg =  4.494949494949495 std =  2.5760110788304695
  File "PyReweighting-1D.py", line 560, in <module>
    main()
  File "PyReweighting-1D.py", line 93, in main
    hist,newedgesX,c1,c2,c3 = reweight_CE(data,hist_min,binsX,discX,dV,T,fit)
  File "PyReweighting-1D.py", line 324, in reweight_CE
    dV_mat[j].append(dV[i])
IndexError: list index out of range

What did i do wrong ?

Thanks for your help for a beginner !

Dr E. Bettler


<OpenPGP_0xA3EFA3AB69BCE823.asc>_______________________________________________
GaMD-discuss mailing list
GaM...@li...
https://lists.sourceforge.net/lists/listinfo/gamd-discuss