Input file
&cntrl
imin = 0, nstlim = 100, dt = 0.001,
irest = 1, ntx = 5, ig = -1,
tempi = 300.0, temp0 = 300.0,
ntc = 2, ntf = 1, tol = 0.00001,
taup =1,
ntwx = 1, ntwe = 0, ntwr = 1, ntpr = 1,
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 = 0.98408, ifsc=1,
timask1=':C3N',timask2='',
scmask1=':C3N', scmask2=''
/
Contents of output is as follows:- (Any suggestions on how to handle this error)
default_name
begin time read from input coords = 11.000 ps
Molecule 2 is completely softcore and skipped for C.O.M..
Number of triangulated 3-point waters found: 13086
Number of shake restraints removed in TI region 1 : 0
Number of shake restraints removed in TI region 2 : 0
Sum of charges for TI region 1 = -0.00000013
Forcing neutrality...
Sum of charges for TI region 2 = -0.00000013
Forcing neutrality...
| Dynamic Memory, Types Used:
| Reals 2537388
| Integers 2301103
| Nonbonded Pairs Initial Allocation: 13259596
| GPU memory information (estimate):
| KB of GPU memory in use: 0
| KB of CPU memory in use: 0
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
DOF for the SC part 1 of the system: 15
SHAKE constraints in the SC region: 3
| TI region 1
NSTEP = 1 TIME(PS) = 11.001 TEMP(K) =********* PRESS = 32007.7
Etot = ************** EKtot = ************** EPtot = 183943650.3992
BOND = 2837.0518 ANGLE = 7047.9762 DIHED = 4792.9393
1-4 NB = 1327.3364 1-4 EEL = 13132.7744 VDWAALS = 80.0258
EELEC = -52969.9741 EHBOND = 0.0000 RESTRAINT = 183967402.2694
EAMBER (non-restraint) = -23751.8702
EKCMT = 1503643.8000 VIRIAL = 16259.3791 VOLUME = 2152243.0090
Density = 0.2075
DV/DL = 17.6627
------------------------------------------------------------------------------
Softcore part of the system: 6 atoms, TEMP(K) = **************
SC_Etot= *********** SC_EKtot= *********** SC_EPtot = ***********
SC_BOND= *********** SC_ANGLE= 187.7787 SC_DIHED = 0.0000
SC_14NB= 0.0000 SC_14EEL= -0.0644 SC_VDW = 0.0000
SC_EEL = 0.0000
SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000
SC_EEL_DER= -0.0254 SC_VDW_DER= -0.0788 SC_DERIV = -0.1042
------------------------------------------------------------------------------
| TI region 2
NSTEP = 1 TIME(PS) = 11.001 TEMP(K) =********* PRESS = 32007.7
Etot = ************** EKtot = ************** EPtot = 183943650.3992
BOND = 2837.0518 ANGLE = 7047.9762 DIHED = 4792.9393
1-4 NB = 1327.3364 1-4 EEL = 13132.7744 VDWAALS = 80.0258
EELEC = -52969.9741 EHBOND = 0.0000 RESTRAINT = 183967402.2694
EAMBER (non-restraint) = -23751.8702
EKCMT = 1503643.8000 VIRIAL = 16259.3791 VOLUME = 2152243.0090
Density = 0.2074
DV/DL = 17.6627
------------------------------------------------------------------------------
From: Debarati DasGupta<mailto:debarati_dasgupta.hotmail.com>
Sent: Friday, December 6, 2019 8:24 AM
To: AMBER Mailing List<mailto:amber.ambermd.org>
Subject: Re: [AMBER] help on this error
Thank you for the helpful reply.
I will try with dt =0.001 instead of dt=0.002
Also will update you of my results with a nstlim=10 and ntpr=1
Will post my results here.
Sent from Mail<
https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10
From: Josh Berryman<mailto:the.real.josh.berryman.gmail.com>
Sent: 06 December 2019 16:52
To: AMBER Mailing List<mailto:amber.ambermd.org>
Subject: Re: [AMBER] help on this error
Just a note, sometimes if your equilibration isn't working on GPU the
easiest step can be to use a different CUDA executable (you should find
several different precision-levels in $AMBERHOME/bin) or to give the input
file to pmemd. Cuda is optimised for speed and can act wacky at larger
forces than those normally encountered in everyday equilibrium MD.
Another lazy fix is to insert an extra equilibration step before the
problematic one, exactly the same but with a much smaller timestep or a
much larger gamma_ln, or both.
Finally note that TI calculations with ifsc are supposed to be smooth and
stable, but they still aren't as reliably smooth as regular non-perturbed
Hamiltonians. If all else fails you might find for some systems that
certain lambda points unavoidably need a smaller timestep.
Josh Berryman
Uni Luxembourg
On Tue, 3 Dec 2019 at 23:06, Debarati DasGupta <
debarati_dasgupta.hotmail.com> wrote:
> 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 Fri Dec 06 2019 - 13:30:02 PST
