What is your reference structure? And what is the initial restraint energy
in the mdout file?
On Wed, Sep 8, 2021, 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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Received on Wed Sep 08 2021 - 03:30:03 PDT
