[AMBER] TI production runs(20ns) NVT query

From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
Date: Thu, 21 May 2020 14:05:42 +0000

Hello,
I just started with my production runs of TI and I wanted to share my 20ns of NVT prod input file.
This is the last step in TI runs after 2ns of NPT equilibration.
Do I need to do 2 steps for disappearing charges and then vdw? I thought if ifsc=1, these 2 steps are taken care of in 1 single step?
Also, my ligand is a 10 atom system (pyrimidine), and its neutral, I m not sure how to disappear charges on it.
Any feedback will definitely help.
Also sincere thanks to Dr Lin for his advice; after applying the SC-patch in AMBER18, I am able to do 2ns of NPT on GPUs (for like 10 out 12 lambdas). Thatís some progress and saving me a lot of time.
Regards,
Debarati

 As an example I have attached input file pertaining to clambda=0.0080, I have 11 other input files for the other lambda parameters.


&cntrl
    imin = 0, nstlim = 20000000, dt = 0.001,
    irest = 1, ntx = 5, ig = -1,
    tempi = 300.0, temp0 = 300.0,
    ntwx = 10000, ntwe = 1000, ntwr = 1000, ntpr = 1000,ntwv=-1, ntave =100,
    cut = 11.0,
    ntt =3, ntb = 1, ntp = 0, gamma_ln=2, iwrap = 1,
    ntc = 1, ntf = 1, tol = 0.00001,
    nsnb = 10, nscm = 10,
    ioutfm=1,
    taup = 1,
    ntr=1, restraintmask=':1P3', restraint_wt = 20.00,
    icfe = 1, clambda = 0.008, ifsc=1,
    timask1=':1P3',timask2='',
    scmask1=':1P3í, scmask2=''
&end
&ewald
   skinnb=2, nfft1=96, nfft2=96, nfft3=96,
/

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Received on Thu May 21 2020 - 07:30:02 PDT
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