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 - 04:00:02 PDT
