No obvious problems at step 28000. In general, you could save a restrt
at that point, then run with ntpr,ntwx=1 so you can analyze what went
wrong in order to learn the most.
After that recorded step, before the next 500 steps are done, the vlimit
is exceeded, and the inscrutable "i and j" here are atoms,
> iter_cnt, my_bond_idx, i and j are : 4 2801 5764 5774
so likely there is a bond or superposition/vdw problem. Typically this
has to do with a self-defined residue, and then either it's an error or
a subtle case that you will need to describe to get help (think strongly
electronegative atoms).
Bill
“Don’t think of it as the warmest month of August in California in
the last century,” he wrote. “Think of it as one of the coolest
months of August in California in the next century.”
On 9/23/20 3:38 AM, R A Jeyaram 16PHD0482 wrote:
> Dear Amber Users,
>
> I am doing MD simulation on the protein-ligand complex system.
> During the heating stage 2, I got an error: vlimit exceeded for step
> 28155; vmax = 147.3455
>
> Coordinate resetting cannot be accomplished, deviation is too large
> iter_cnt, my_bond_idx, i and j are : 4 2801 5764 5774
>
> The simulation details are given below:
> Number of protein atoms: 5753 (385 residues)
> Number of ligand atoms: 41 (1 residue)
> Number of Counter ions: 7
> TIP3P box size : 10 angstroms
>
> heating stage 2
> &cntrl
> imin=0,irest=1,ntx=5,
> nstlim=100000,dt=0.002,
> ntc=2,ntf=2,
> cut=8.0, ntb=2, ntp=1, taup=1.0,
> ntpr=500, ntwx=500,
> ntt=3, gamma_ln=2.0,
> temp0=300.0, ig=-1,
> ntr=1, restraintmask=':1-393',
> restraint_wt=2.0,
> /
>
> Herewith I am attaching the input and output file of the heating stage 2.
> Help me to solve the issue.
>
> Thanks and Regards
> R. A. Jeyaram
> Vellore Institute of Technology
> Tamil Nadu, India.
>
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Received on Wed Sep 23 2020 - 04:00:04 PDT
