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From: Debarati DasGupta<mailto:debarati_dasgupta.hotmail.com>
Sent: 27 November 2020 12:37
To: Adrian Roitberg<mailto:roitberg.ufl.edu>
Subject: RE: [AMBER] AMBER20 TI calculations
Hello Prof Roitberg,
Thanks for your reply, really appreciate it.
SO this is the input file (for clambda=0.20634) which leads me to the unstable simulation:
&cntrl
imin = 0, nstlim = 100000, dt = 0.001,
irest = 0, ntx = 1, ig = -1,
tempi = 0.0, temp0 = 50.0
ntc = 1, ntf = 1, tol = 0.00001,
nsnb = 10, nscm = 10,
ioutfm=1,
taup = 1,
ntwx = 100, ntwe = 100, ntwr = 100, ntpr = 100, ntwv=-1, ntave = 100,
cut = 11.0, iwrap = 1,
ntt =3, ntb = 1, ntp = 0, gamma_ln=1.0,
nscm = 0,
icfe = 1, clambda=0.20634, ifsc=1,
timask1=':IPA',timask2= '', scalpha = 0.1, scbeta = 50.0,
scmask1 = ':IPA', scmask2 = '',
nmropt=1,
/
&wt type='DUMPFREQ', istep1=1, /
&wt type='END', /
DISANG=output.disang
DUMPAVE=dist_0.20634.dat
LISTIN=POUT
LISTOUT=POUT
/
&ewald
skinnb=2, nfft1=96, nfft2=96, nfft3=96,
/
&wt type='TEMP0', istep1=0, istep2=90000, value1=0.0, value2=50.0 /
&wt type='TEMP0', istep1=90001, istep2=100000, value1=50.0, value2=50.0 /
&wt type='END' /
Also, when I use harmonic restraints (ntr=1), the simulation does not crash.
I am running a 10 step heating without restraints to check on the run.
Do you want me to provide you the prmtop and inpcrd file?
Thanks
Debarati
From: Adrian Roitberg<mailto:roitberg.ufl.edu>
Sent: 27 November 2020 12:21
To: AMBER Mailing List<mailto:amber.ambermd.org>; Debarati DasGupta<mailto:debarati_dasgupta.hotmail.com>
Subject: Re: [AMBER] AMBER20 TI calculations
Hard to tell without more details, but...
You are getting warning about NMR restraints, I would check those first.
What happens if you take the restraints out just to check on the run ?
Your box size seems to be immense. I very much doubt that your system is 91 MICROMETERS to the side !
adrian
On 11/27/20 12:15 PM, Debarati DasGupta wrote:
[External Email]
Hello everyone,
I am running an absolute binding free energy calculation on a ABL kinase system ( ligand is isopropanol), I have applied distance based restraints to keep the ligand in the pocket:
However, after minimization, the system gets unstable in the temperature ramping simulation I get this: ( see picture below). Any ideas/thoughts on how to prevent this?
I have used softcore potentials and I am doing a stepwise de-charge, then disappearing the LJ interactions.
Thanks
Debarati
[cid:image001.png.01D6C4B6.D8F0CCC0]
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Dr. Adrian E. Roitberg
V.T. and Louise Jackson Professor in Chemistry
Department of Chemistry
University of Florida
roitberg.ufl.edu<mailto:roitberg.ufl.edu>
352-392-6972
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Received on Fri Nov 27 2020 - 10:00:02 PST
