Hi,
I've recently helped develop a protocol for preparing systems for
explicitly solvated MD that you may find useful:
https://aip.scitation.org/doi/abs/10.1063/5.0013849
I've also written a script that implements this protocol for Amber:
https://github.com/drroe/AmberMdPrep
Feel free to give it a try, it's still fairly rough around the edges,
so use with caution.
-Dan
On Wed, Sep 23, 2020 at 6:36 AM R A Jeyaram 16PHD0482
<ra.jeyaram2016.vitstudent.ac.in> 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 - 04:00:03 PDT
