Independently of your ATP position, your system may explode or show
LINCS warnings if you use pressure and temperature coupling. I had these
problem, and corrected it removing the pressure coupling. Pressure
coupling will let your system expand in response to the heat, and if the
positions are restrained, it`s going to develop a big force that makes
your system explode, as happens in real life.
nikhil damle escribió:
Hi
When i subjected the complex to EM, it gave following warning:
"1-4 interaction between 3063 and 3068 at distance 1.436 which is
larger than the 1-4 table size 1.000 nm. These are ignored for the
rest of the simulation. This usually means your system is exploding,"
These atoms are oxygens of 2 phosphate grps ofATP. Later if i
continue, with SD it converges with less precision. so i applied CG.
It converged. But when I carry out position-restrained dynamics, it
gave # of LINCS warnings in both cases. Does this mean EM is not done
properly ? How should I address this ?
Regards,
Nikhil
------------------------------------------------------------------------
*From:* Mark Abraham <mark.abra...@anu.edu.au>
*To:* Discussion list for GROMACS users <gmx-users@gromacs.org>
*Sent:* Tuesday, 23 June, 2009 9:10:15 PM
*Subject:* Re: [gmx-users] simulation of protein in presence of ATP
nikhil damle wrote:
> OK till here done ! the pdb file generated for EM should have ATP
molecule @proper position as input .top file has the ATP.itp included.
It did not have. If I do -ci it would randomly replace the solvent. I
want ATP @ its proper location. how do i do this ?
Like I implied several emails ago, you should order the [molecules]
entries according to the coordinate file, as normal.
Mark
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