Dear Prof. Carlos Simmerling,
The comments you said help me a lot.
I solved my problem by changing the reference file.
Sincerely yours,
Thank you.
2021년 9월 10일 (금) 오전 6:40, Carlos Simmerling <carlos.simmerling.gmail.com>님이
작성:
> I checked the files that you shared offlist.
>
> the TI step doesn't match what you provided here, so I can comment on what
> you sent but it might not match this problem since it's not the same
> output.
>
> your TI output step says this about your input file:
>
> ntr = 1, restraint_wt = 10.0,
>
> restraintmask=':72,181.CA',
>
>
> so you are restraining 2 atoms. when you look at the initial energy you see
> this:
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
> 0.0
> Etot = 10714.2446 EKtot = 0.0000 EPtot =
> 10714.2446
> BOND = 413.3732 ANGLE = 1011.9453 DIHED =
> 1800.0072
> 1-4 NB = 548.8708 1-4 EEL = 11331.5321 VDWAALS =
> 48069.0806
> EELEC = -387183.3524 EHBOND = 0.0000 RESTRAINT =
> 334722.7877
> EAMBER (non-restraint) = -324008.5431
> DV/DL = 82.1952
>
>
>
> the restraint energy is extremely high, and the system will be unstable.
> This usually means that your inpcrd and your refc do not match.
> Checking your file assignments it shows that your initial coordinates are
> heat.rst7, but your reference is ti.rst7. These must differ significantly
> in the positions of those 2 atoms that you want to restrain.
> Your files don't say how you generated ti.rst7.
>
> | INPCRD: heat.rst7
>
> | PARM: ti.parm7
>
> | RESTRT: ti001.rst7
>
> | REFC: ti.rst7
>
>
> On Wed, Sep 8, 2021 at 4:44 AM LEO LIM <ihc950213.gmail.com> wrote:
>
> > Dear Amber MD users,
> >
> > Hello,
> > I am using Amber 18 for Thermodynamic Integration (TI) with GPU (TITAN
> RTX
> > 24GB).
> >
> > I want to fix alpha carbon in #72 residue as a position restraint,
> > but I got the below error message.
> > "cudaMemcpy GpuBuffer::Download failed an illegal memory access was
> > encountered"
> >
> > I successfully simulated the same system without constraints,
> > so I think that it is not related to GPU memory.
> >
> > The constraint I used is that ntr = 1, restraint_wt = 10.0,
> > restraintmask=':72.CA'
> >
> > This is my input file below.
> > What should I do to add the positional constraints in TI simulation ?
> >
> > Sincerely,
> > Thank you.
> >
> > > input file.
> > TI simulation
> > &cntrl
> > imin = 0, nstlim = 20000, irest = 0, ntx = 1, dt = 0.002,
> > ntt = 3, temp0 = 300.0, gamma_ln = 2.0, ig = -1,
> > ntc = 2, ntf = 1,
> > ntb = 1,
> > ioutfm = 1, iwrap = 1,
> > ntwe = 1000, ntwx = 1000, ntpr = 1000, ntwr = 1000,
> >
> > ntr = 1, restraint_wt = 10.0,
> > restraintmask=':72.CA',
> >
> > icfe = 1, ifsc = 1, clambda = %L%, scalpha = 0.5, scbeta = 12.0,
> > logdvdl = 1,
> > ifmbar = 1, mbar_states = 11,
> > mbar_lambda = 0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0,
> > timask1 = ':8', timask2 = ':109',
> > scmask1 = ':8', scmask2 = ':109',
> > /
> >
> > &ewald
> > /
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> >
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Received on Fri Sep 10 2021 - 05:30:02 PDT
