Again I remind you, please do not include the entire text of the digest when
posting messages to the list.
rituraj purohit wrote:
Dear Friends,
I am geting following error during pr.mdp
-------
Warning: 1-4 interaction between 11 and 18 at distance 1.301 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,
if not, you should increase table-extension in your mdp file
---------
I am running following commands.
Are they? In the genion step, you are adding two Cl- ions. You say your system
has a net -42 charge. If you are adding more negative charges, please refer to
my post from yesterday. Otherwise, provide accurate commands for what you are
really doing.
-----
pdb2gmx -ignh -ff G43a1 -f xxx.pdb -o fws.pdb -p fws.top -water spce
editconf -bt cubic -f fws.pdb -o fws.pdb -d 1
genbox -cp fws.pdb -cs spc216.gro -o fws_b4em.pdb -p fws.top
grompp -f em.mdp -c fws_b4em.pdb -p fws.top -o fws_em.tpr
genion -s fws_em.tpr -o fws_ion.pdb -nname CL- -nn 2 -g fws_ion.log
grompp -f em.mdp -c fws_ion.pdb -p fws.top -o fws_em.tpr
mdrun -v -s fws_em.tpr -o fws_em.trr -c fws_b4pr.pdb -e em.edr -g em.log &
grompp -f pr.mdp -c fws_b4pr.pdb -p fws.top -o pr.tpr -maxwarn 3
What warnings are you ignoring from grompp with -maxwarn 3? If this is indeed
your real command...
mdrun -s pr.tpr -o pr.trr -c fws_b4md.pdb -e pr.edr -g pr.log
------
and my pr.mdp is as follows...
-------
<snip>
Nothing in the .mdp file seems problematic.
What is theproblem i am not getting, i gone through old gmx list and i
got their may be problem of force field,
Which force field is suitable for my protein (having two chain & net
charge of -42 e) in water ?
There are numerous reasons for system instability. Blaming it on the force
field is about the last that I would try, however, seeing as folks have been
using ffG43a1 for many years on many systems. Since your system is crashing
during equilibration, the more likely problem is that your energy minimization
was insufficient.
-Justin
Thanks in advanced :)
--
========================================
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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