Hi Prof Case,
I am providing details of whatever setup I did for my TI absolute free energy calculation.
My lambda windows for absolute free energy calc is as follows:
0.01592
0.08198
0.19331
0.33787
0.5
0.66213
0.80669
0.91802
0.98408
My input files for minimization, heating and equilibration are as follows:
Min.in
minimisation
&cntrl
imin = 1, ntmin = 2,
maxcyc = 10000,
ntpr = 20, ntwe = 20,
ntb = 1,
ntr = 1, restraint_wt = 200.00,
restraintmask='!:WAT & !.H=',
icfe = 1, ifsc = 1, clambda = 0.01592, scalpha = 0.5, scbeta = 12.0,
logdvdl = 0,
timask1 = ':C3N', timask2 = '',
scmask1 = ':C3N', scmask2 = ''
/
&ewald
/
Heat1.in
heating
&cntrl
imin = 0, nstlim = 10000, irest = 0, ntx = 1, dt = 0.001,
nmropt = 1,
ntt = 1, temp0 = 100.0, tempi = 50.0, tautp = 1.0,
ntb = 1, tol = 0.00001,
ntc = 2, ntf = 1,
ioutfm = 1, iwrap = 1,
ntwe = 1000, ntwx = 1000, ntpr = 1000, ntwr = 5000,
ntr = 1, restraint_wt = 200.00,
restraintmask='!:WAT & !.H=',
icfe = 1, ifsc = 1, clambda = 0.01592, scalpha = 0.5, scbeta = 12.0,
logdvdl = 0,
timask1 = ':C3N', timask2 = '',
scmask1 = ':C3N', scmask2 = ''
/
&ewald
/
&wt
type='TEMP0',
istep1 = 0, istep2 = 8000,
value1 = 50.0, value2 = 100.0
/
&wt type = 'END'
/
Heat2.in
heating
&cntrl
imin = 0, nstlim = 10000, irest = 0, ntx = 1, dt = 0.001,
nmropt = 1,
ntt = 1, temp0 = 200.0, tempi = 100.0, tautp = 1.0,
ntb = 1, tol = 0.00001,
ntc = 2, ntf = 1,
ioutfm = 1, iwrap = 1,
ntwe = 1000, ntwx = 1000, ntpr = 1000, ntwr = 5000,
ntr = 1, restraint_wt = 200.00,
restraintmask=':287',
icfe = 1, ifsc = 1, clambda = 0.01592, scalpha = 0.5, scbeta = 12.0,
logdvdl = 0,
timask1 = ':C3N', timask2 = '',
scmask1 = ':C3N', scmask2 = ''
/
&ewald
/
&wt
type='TEMP0',
istep1 = 0, istep2 = 8000,
value1 = 100.0, value2 = 200.0
/
&wt type = 'END'
/
Heat3.in
heating
&cntrl
imin = 0, nstlim = 10000, irest = 0, ntx = 1, dt = 0.001,
nmropt = 1,
ntt = 1, temp0 = 300.0, tempi = 200.0, tautp = 1.0,
ntb = 1, tol = 0.00001,
ntc = 2, ntf = 1,
ioutfm = 1, iwrap = 1,
ntwe = 1000, ntwx = 1000, ntpr = 1000, ntwr = 5000,
ntr = 1, restraint_wt = 200.00,
restraintmask=':287',
icfe = 1, ifsc = 1, clambda = 0.01592, scalpha = 0.5, scbeta = 12.0,
logdvdl = 0,
timask1 = ':C3N', timask2 = '',
scmask1 = ':C3N', scmask2 = ''
/
&ewald
/
&wt
type='TEMP0',
istep1 = 0, istep2 = 8000,
value1 = 200.0, value2 = 300.0
/
&wt type = 'END'
/
Equil1A.in
&cntrl
imin = 0, nstlim = 1000000, dt = 0.001,
irest = 1, ntx = 5, ig = -1,
tempi = 300.0, temp0 = 300.0,
ntc = 2, ntf = 1, tol = 0.00001,
taup = 0.1,
ntwx = 10000, ntwe = 0, ntwr = 1000, ntpr = 1000,
cut = 10.0, iwrap = 1,
ntt =3, ntb = 2, ntp = 1, gamma_ln=1.0,
nscm = 0,
ntr=1, restraintmask=':287', restraint_wt=100,
icfe = 1, clambda=0.01592, ifsc=1,
timask1=':C3N',timask2='',
scmask1 = ':C3N', scmask2 = ''
/
Equil1B.in
&cntrl
imin = 0, nstlim = 1000000, dt = 0.002,
irest = 1, ntx = 5, ig = -1,
tempi = 300.0, temp0 = 300.0,
ntc = 2, ntf = 1, tol = 0.00001,
taup = 0.1,
ntwx = 10, ntwe = 0, ntwr = 10, ntpr = 10,
cut = 10.0, iwrap = 1,
ntt =3, ntb = 2, ntp = 1, gamma_ln=1.0,
nscm = 0,
ntr=1, restraintmask=':287', restraint_wt=100,
icfe = 1, clambda=0.01592, ifsc=1,
timask1 = ':C3N',timask2 = '',
scmask1 = ':C3N', scmask2 = ''
/
My protein is a 160 residue kinase+ my ligand is a small molecule( 10atoms)
Everytime I do run the last step of equlibriation equil1B.in I get this error,
Hostname = grape1
Date = Mon Dec 2 17:06:33 EST 2019
SLURM_GPUFILE ...
gpuNum=
cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered
Any help will be really useful.
I have provided all the steps I did, this is only for my lambda 0.01592
I need to sort it out before running other lambdas as I need the rst files from 0.01592 to run at higher lambdas.
Any help ?
Thanks
________________________________________________________________________________________________________________________________________________________________________
From: David Case<mailto:david.case.rutgers.edu>
Sent: Friday, November 29, 2019 9:10 PM
To: AMBER Mailing List<mailto:amber.ambermd.org>
Subject: Re: [AMBER] help on this error
On Fri, Nov 29, 2019, Debarati DasGupta wrote:
>vlimit exceeded for step 0; vmax = 36.5121
The fact that you get this error on step 0 suggests that something has
changed from the previous run, that is changing the energy and
gradients.
Try a "short" (10 step run) with ntpr=1. Compare the energies on step 1
with the final energies from the previous runs. Try to figure out what
is changing.
>In my equlibriation steps in TI, in the final step I always am getting
>this error.
The problem is that we don't know what you mean by the "final step".
(There is no single way to carry out equilibration.)
You don't have to tell us: try to figure out what is different between
the steps that "work" and the one that gives the error you cite above.
...good luck...dac
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Received on Tue Dec 03 2019 - 14:30:02 PST
