[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 
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...
> -------


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.


> 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


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