nikhil damle wrote:
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 ?
Some useful links:
http://oldwiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings
http://oldwiki.gromacs.org/index.php/blowing_up
-Justin
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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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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