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
> /
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Sep 09 2021 - 15:00:03 PDT
