Many thanks. I have repeated simulations with iwrap=0 in the past and just
now, but the issue remains the same:
https://www.dropbox.com/s/13cgyo3legiimlc/Gamd_err1.png?dl=0
Suddenly, two ligands start distorting within a few hundred steps, and I
still do not understand what's going wrong. cMD works fine, and I am
starting these game simulations using the restart file from 1-microsecond
cMD in pmemd.cuda. I have also tried up to 100ns cMD using CPU code and
then restarting gamd but the issue remains the same.
Do you think there is any mistake I am making with the MD input setting?
&cntrl
imin=0, irest=1, ntx=5,
ntt=3, gamma_ln=1.0, temp0=300,
ntpr=50, ntwx=50, ntwr=50000,
cut=9.0, nstlim=500000, dt=0.001,
ntc=1, ntf=1,
iwrap=0, barostat=2,
ntp=1, pres0=1.0,
ntxo=2, ioutfm=1,
igamd = 11, irest_gamd = 0,
ntcmd = 700000, nteb = 27300000, ntave = 140000,
ntcmdprep = 280000, ntebprep = 280000,
sigma0P = 4.0, sigma0D = 6.0, iEP = 2, iED=1,
icfe = 1, ifsc = 1, gti_cpu_output = 0, gti_add_sc = 1,
timask1 = ':1-2', scmask1 = ':1-2',
timask2 = '', scmask2 = '',
ibblig = 1, nlig = 10, atom_p = 667, atom_l = 19, dblig = 3.7,
&end
Mish
On Wed, May 24, 2023 at 1:00 PM David A Case <david.case.rutgers.edu> wrote:
> On Wed, May 24, 2023, mish via AMBER wrote:
>
> >The problem seems to occur when one of the free ligands is close to the
> >boundary, and wrapping it back in the box completely messes up the system.
> >Any suggestions on how to prevent it?
>
> It's certainly worth setting iwrap to the default value of zero. If you
> look at the description of this variable (section 21.6.3 in the Reference
> Manual), you'll see that there are very few (modern) circumstances in which
> a non-zero value is useful. (If you *do* need to wrap the simulation into
> a
> periodic box, say for visualization, it is better to use cpptraj for that
> purpose, since cpptraj is much more flexible.)
>
> It is possible (but outside my bailiwick) that ligand GaMD does is not
> fully
> periodic. But take care, especially if you have some reason for setting
> iwrap=1 in the first place.
>
> ....dac
>
>
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Received on Wed May 24 2023 - 15:00:02 PDT
