[gmx-users] How to select Force field
Justin A. Lemkul
jalemkul at vt.edu
Sun Aug 30 17:33:54 CEST 2009
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
> 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...
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
> Thanks in advanced :)
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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